Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Likelihood Functions: Functions constructed from a statistical model and a set of observed data which give the probability of that data for various values of the unknown model parameters. Those parameter values that maximize the probability are the maximum likelihood estimates of the parameters.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.DNA, Mitochondrial: Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Bayes Theorem: A theorem in probability theory named for Thomas Bayes (1702-1761). In epidemiology, it is used to obtain the probability of disease in a group of people with some characteristic on the basis of the overall rate of that disease and of the likelihood of that characteristic in healthy and diseased individuals. The most familiar application is in clinical decision analysis where it is used for estimating the probability of a particular diagnosis given the appearance of some symptoms or test result.Fossils: Remains, impressions, or traces of animals or plants of past geological times which have been preserved in the earth's crust.DNA, Ribosomal Spacer: The intergenic DNA segments that are between the ribosomal RNA genes (internal transcribed spacers) and between the tandemly repeated units of rDNA (external transcribed spacers and nontranscribed spacers).DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.Genetic Speciation: The splitting of an ancestral species into daughter species that coexist in time (King, Dictionary of Genetics, 6th ed). Causal factors may include geographic isolation, HABITAT geometry, migration, REPRODUCTIVE ISOLATION, random GENETIC DRIFT and MUTATION.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.RNA, Ribosomal, 18S: Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.Genetic Variation: Genotypic differences observed among individuals in a population.DNA, Chloroplast: Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Phylogeography: A field of study concerned with the principles and processes governing the geographic distributions of genealogical lineages, especially those within and among closely related species. (Avise, J.C., Phylogeography: The History and Formation of Species. Harvard University Press, 2000)RNA, Ribosomal, 28S: Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.Genome, Mitochondrial: The genetic complement of MITOCHONDRIA as represented in their DNA.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Classification: The systematic arrangement of entities in any field into categories classes based on common characteristics such as properties, morphology, subject matter, etc.Gene Transfer, Horizontal: The naturally occurring transmission of genetic information between organisms, related or unrelated, circumventing parent-to-offspring transmission. Horizontal gene transfer may occur via a variety of naturally occurring processes such as GENETIC CONJUGATION; GENETIC TRANSDUCTION; and TRANSFECTION. It may result in a change of the recipient organism's genetic composition (TRANSFORMATION, GENETIC).Mammals: Warm-blooded vertebrate animals belonging to the class Mammalia, including all that possess hair and suckle their young.Angiosperms: Members of the group of vascular plants which bear flowers. They are differentiated from GYMNOSPERMS by their production of seeds within a closed chamber (OVARY, PLANT). The Angiosperms division is composed of two classes, the monocotyledons (Liliopsida) and dicotyledons (Magnoliopsida). Angiosperms represent approximately 80% of all known living plants.Genes, Mitochondrial: Genes that are located on the MITOCHONDRIAL DNA. Mitochondrial inheritance is often referred to as maternal inheritance but should be differentiated from maternal inheritance that is transmitted chromosomally.Geography: The science dealing with the earth and its life, especially the description of land, sea, and air and the distribution of plant and animal life, including humanity and human industries with reference to the mutual relations of these elements. (From Webster, 3d ed)Gymnosperms: Gymnosperms are a group of vascular plants whose seeds are not enclosed by a ripened ovary (fruit), in contrast to ANGIOSPERMS whose seeds are surrounded by an ovary wall. The seeds of many gymnosperms (literally, "naked seed") are borne in cones and are not visible. Taxonomists now recognize four distinct divisions of extant gymnospermous plants (CONIFEROPHYTA; CYCADOPHYTA; GINKGOPHYTA; and GNETOPHYTA).Invertebrates: Animals that have no spinal column.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Plastids: Self-replicating cytoplasmic organelles of plant and algal cells that contain pigments and may synthesize and accumulate various substances. PLASTID GENOMES are used in phylogenetic studies.Arthropods: Members of the phylum Arthropoda, composed of organisms having a hard, jointed exoskeleton and paired jointed legs. It includes the class INSECTS and the subclass ARACHNIDA, many species of which are important medically as parasites or as vectors of organisms capable of causing disease in man.RNA, Ribosomal: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)PrimatesMultigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Biodiversity: The variety of all native living organisms and their various forms and interrelationships.Gene Duplication: Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.Eukaryota: One of the three domains of life (the others being BACTERIA and ARCHAEA), also called Eukarya. These are organisms whose cells are enclosed in membranes and possess a nucleus. They comprise almost all multicellular and many unicellular organisms, and are traditionally divided into groups (sometimes called kingdoms) including ANIMALS; PLANTS; FUNGI; and various algae and other taxa that were previously part of the old kingdom Protista.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Birds: Warm-blooded VERTEBRATES possessing FEATHERS and belonging to the class Aves.Vertebrates: Animals having a vertebral column, members of the phylum Chordata, subphylum Craniata comprising mammals, birds, reptiles, amphibians, and fishes.Genes, rRNA: Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPERONS dispersed throughout the GENOME, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.Extinction, Biological: The ceasing of existence of a species or taxonomic groups of organisms.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Symbiosis: The relationship between two different species of organisms that are interdependent; each gains benefits from the other or a relationship between different species where both of the organisms in question benefit from the presence of the other.Plants: Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Ascomycota: A phylum of fungi which have cross-walls or septa in the mycelium. The perfect state is characterized by the formation of a saclike cell (ascus) containing ascospores. Most pathogenic fungi with a known perfect state belong to this phylum.Anthocerotophyta: A plant division that includes hornworts, named for the horn-like appearance of the spore-producing plant (sporophyte).Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Strepsirhini: A suborder of PRIMATES consisting of the following five families: CHEIROGALEIDAE; Daubentoniidae; Indriidae; LEMURIDAE; and LORISIDAE.Archaea: One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.Ecosystem: A functional system which includes the organisms of a natural community together with their environment. (McGraw Hill Dictionary of Scientific and Technical Terms, 4th ed)DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Bacteria: One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.Peptide Elongation Factor 1: Peptide elongation factor 1 is a multisubunit protein that is responsible for the GTP-dependent binding of aminoacyl-tRNAs to eukaryotic ribosomes. The alpha subunit (EF-1alpha) binds aminoacyl-tRNA and transfers it to the ribosome in a process linked to GTP hydrolysis. The beta and delta subunits (EF-1beta, EF-1delta) are involved in exchanging GDP for GTP. The gamma subunit (EF-1gamma) is a structural component.Platyhelminths: A phylum of acoelomate, bilaterally symmetrical flatworms, without a definite anus. It includes three classes: Cestoda, Turbellaria, and Trematoda.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Sequence Homology: The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.Gene Order: The sequential location of genes on a chromosome.Cetacea: An order of wholly aquatic MAMMALS occurring in all the OCEANS and adjoining seas of the world, as well as in certain river systems. They feed generally on FISHES, cephalopods, and crustaceans. Most are gregarious and most have a relatively long period of parental care and maturation. Included are DOLPHINS; PORPOISES; and WHALES. (From Walker's Mammals of the World, 5th ed, pp969-70)Fishes: A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales.Genes, Archaeal: The functional genetic units of ARCHAEA.LizardsRhodophyta: Plants of the division Rhodophyta, commonly known as red algae, in which the red pigment (PHYCOERYTHRIN) predominates. However, if this pigment is destroyed, the algae can appear purple, brown, green, or yellow. Two important substances found in the cell walls of red algae are AGAR and CARRAGEENAN. Some rhodophyta are notable SEAWEED (macroalgae).Ciliophora: A phylum of EUKARYOTES characterized by the presence of cilia at some time during the life cycle. It comprises three classes: KINETOFRAGMINOPHOREA; OLIGOHYMENOPHOREA; and POLYMENOPHOREA.Paleontology: The study of early forms of life through fossil remains.DNA, Intergenic: Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.Insects: The class Insecta, in the phylum ARTHROPODA, whose members are characterized by division into three parts: head, thorax, and abdomen. They are the dominant group of animals on earth; several hundred thousand different kinds having been described. Three orders, HEMIPTERA; DIPTERA; and SIPHONAPTERA; are of medical interest in that they cause disease in humans and animals. (From Borror et al., An Introduction to the Study of Insects, 4th ed, p1)Hominidae: Family of the suborder HAPLORHINI (Anthropoidea) comprising bipedal primate MAMMALS. It includes modern man (HOMO SAPIENS) and the great apes: gorillas (GORILLA GORILLA), chimpanzees (PAN PANISCUS and PAN TROGLODYTES), and orangutans (PONGO PYGMAEUS).Fungi: A kingdom of eukaryotic, heterotrophic organisms that live parasitically as saprobes, including MUSHROOMS; YEASTS; smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi, commonly known as molds, refer to those that grow as multicellular colonies.Genes, Chloroplast: Those nucleic acid sequences that function as units of heredity which are located within the CHLOROPLAST DNA.RNA, Ribosomal, 5.8S: Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.Gastropoda: A class in the phylum MOLLUSCA comprised of SNAILS and slugs. The former have coiled external shells and the latter usually lack shells.Madagascar: One of the Indian Ocean Islands off the southeast coast of Africa. Its capital is Antananarivo. It was formerly called the Malagasy Republic. Discovered by the Portuguese in 1500, its history has been tied predominantly to the French, becoming a French protectorate in 1882, a French colony in 1896, and a territory within the French union in 1946. The Malagasy Republic was established in the French Community in 1958 but it achieved independence in 1960. Its name was changed to Madagascar in 1975. (From Webster's New Geographical Dictionary, 1988, p714)Kinetoplastida: An order of flagellate protozoa. Characteristics include the presence of one or two flagella arising from a depression in the cell body and a single mitochondrion that extends the length of the body.Chlorophyta: A phylum of photosynthetic EUKARYOTA bearing double membrane-bound plastids containing chlorophyll a and b. They comprise the classical green algae, and represent over 7000 species that live in a variety of primarily aquatic habitats. Only about ten percent are marine species, most live in freshwater.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Hylobates: A genus of the family HYLOBATIDAE consisting of six species. The members of this genus inhabit rain forests in southeast Asia. They are arboreal and differ from other anthropoids in the great length of their arms and very slender bodies and limbs. Their major means of locomotion is by swinging from branch to branch by their arms. Hylobates means dweller in the trees. Some authors refer to Symphalangus and Nomascus as Hylobates. The six genera include: H. concolor (crested or black gibbon), H. hoolock (Hoolock gibbon), H. klossii (Kloss's gibbon; dwarf siamang), H. lar (common gibbon), H. pileatus (pileated gibbon), and H. syndactylus (siamang). H. lar is also known as H. agilis (lar gibbon), H. moloch (agile gibbon), and H. muelleri (silvery gibbon).Basidiomycota: A phylum of fungi that produce their sexual spores (basidiospores) on the outside of the basidium. It includes forms commonly known as mushrooms, boletes, puffballs, earthstars, stinkhorns, bird's-nest fungi, jelly fungi, bracket or shelf fungi, and rust and smut fungi.Geology: The science of the earth and other celestial bodies and their history as recorded in the rocks. It includes the study of geologic processes of an area such as rock formations, weathering and erosion, and sedimentation. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Prokaryotic Cells: Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Insectivora: An order of insect eating MAMMALS including MOLES; SHREWS; HEDGEHOGS and tenrecs.Gammaproteobacteria: A group of the proteobacteria comprised of facultatively anaerobic and fermentative gram-negative bacteria.Liliaceae: A monocot family within the order Liliales. This family is divided by some botanists into other families such as Convallariaceae, Hyacinthaceae and Amaryllidaceae. Amaryllidaceae, which have inferior ovaries, includes CRINUM; GALANTHUS; LYCORIS; and NARCISSUS and are known for AMARYLLIDACEAE ALKALOIDS.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Multilocus Sequence Typing: Direct nucleotide sequencing of gene fragments from multiple housekeeping genes for the purpose of phylogenetic analysis, organism identification, and typing of species, strain, serovar, or other distinguishable phylogenetic level.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Asteraceae: A large plant family of the order Asterales, subclass Asteridae, class Magnoliopsida. The family is also known as Compositae. Flower petals are joined near the base and stamens alternate with the corolla lobes. The common name of "daisy" refers to several genera of this family including Aster; CHRYSANTHEMUM; RUDBECKIA; TANACETUM.South AmericaSequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Cryptophyta: A class of EUKARYOTA (traditionally algae), characterized by biflagellated cells and found in both freshwater and marine environments. Pigmentation varies but only one CHLOROPLAST is present. Unique structures include a nucleomorph and ejectosomes.Ribosome Subunits, Small: The small ribonucleoprotein component of RIBOSOMES. It contains the MESSENGER RNA binding site and two TRANSFER RNA binding sites - one for the incoming AMINO ACYL TRNA (A site) and the other (P site) for the peptidyl tRNA carrying the elongating peptide chain.Eukaryotic Cells: Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.Crustacea: A large subphylum of mostly marine ARTHROPODS containing over 42,000 species. They include familiar arthropods such as lobsters (NEPHROPIDAE), crabs (BRACHYURA), shrimp (PENAEIDAE), and barnacles (THORACICA).Ficus: A plant genus of the family MORACEAE. It is the source of the familiar fig fruit and the latex from this tree contains FICAIN.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Genome, Plastid: The genetic complement of PLASTIDS as represented in their DNA.PanamaProteobacteria: A phylum of bacteria consisting of the purple bacteria and their relatives which form a branch of the eubacterial tree. This group of predominantly gram-negative bacteria is classified based on homology of equivalent nucleotide sequences of 16S ribosomal RNA or by hybridization of ribosomal RNA or DNA with 16S and 23S ribosomal RNA.Haplotypes: The genetic constitution of individuals with respect to one member of a pair of allelic genes, or sets of genes that are closely linked and tend to be inherited together such as those of the MAJOR HISTOCOMPATIBILITY COMPLEX.Genes, Bacterial: The functional hereditary units of BACTERIA.Synteny: The presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Hepatophyta: A plant division. They are simple plants that lack vascular tissue and possess rudimentary rootlike organs (rhizoids). Like MOSSES, liverworts have alternation of generations between haploid gamete-bearing forms (gametophytes) and diploid spore-bearing forms (sporophytes).Genes, Plant: The functional hereditary units of PLANTS.DNA Barcoding, Taxonomic: Techniques for standardizing and expediting taxonomic identification or classification of organisms that are based on deciphering the sequence of one or a few regions of DNA known as the "DNA barcode".Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.Cercopithecidae: The family of Old World monkeys and baboons consisting of two subfamilies: CERCOPITHECINAE and COLOBINAE. They are found in Africa and part of Asia.Asia: The largest of the continents. It was known to the Romans more specifically as what we know today as Asia Minor. The name comes from at least two possible sources: from the Assyrian asu (to rise) or from the Sanskrit usa (dawn), both with reference to its being the land of the rising sun, i.e., eastern as opposed to Europe, to the west. (From Webster's New Geographical Dictionary, 1988, p82 & Room, Brewer's Dictionary of Names, 1992, p34)Short Interspersed Nucleotide Elements: Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats).Geological Phenomena: The inanimate matter of Earth, the structures and properties of this matter, and the processes that affect it.Solanaceae: A plant family of the order Solanales, subclass Asteridae. Among the most important are POTATOES; TOMATOES; CAPSICUM (green and red peppers); TOBACCO; and BELLADONNA.Echinodermata: A phylum of the most familiar marine invertebrates. Its class Stelleroidea contains two subclasses, the Asteroidea (the STARFISH or sea stars) and the Ophiuroidea (the brittle stars, also called basket stars and serpent stars). There are 1500 described species of STARFISH found throughout the world. The second class, Echinoidea, contains about 950 species of SEA URCHINS, heart urchins, and sand dollars. A third class, Holothuroidea, comprises about 900 echinoderms known as SEA CUCUMBERS. Echinoderms are used extensively in biological research. (From Barnes, Invertebrate Zoology, 5th ed, pp773-826)ArtiodactylaGenome, Archaeal: The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.Dictyosteliida: An order of protozoa characterized by their ability to aggregate to form a multicellular pseudoplasmodium, which gives rise to a multispored fruiting body. A stalk tube is present.Alphaproteobacteria: A class in the phylum PROTEOBACTERIA comprised mostly of two major phenotypes: purple non-sulfur bacteria and aerobic bacteriochlorophyll-containing bacteria.Rhizaria: A large supergroup of mostly amoeboid EUKARYOTES whose three main subgroups are CERCOZOA; FORAMINIFERA; and HAPLOSPORIDA. Nearly all of the species possess MITOCHONDRIA and historically many were considered ANIMALS.Body Size: The physical measurements of a body.Rodentia: A mammalian order which consists of 29 families and many genera.Xenarthra: An order of New World mammals characterized by the absence of incisors and canines from among their teeth, and comprising the ARMADILLOS, the SLOTHS, and the anteaters. The order is distinguished from all others by what are known as xenarthrous vertebrae (xenos, strange; arthron, joint): there are secondary, and sometimes even more, articulations between the vertebrae of the lumbar series. The order was formerly called Edentata. (From Random House Unabridged Dictionary, 2d ed; Walker's Mammals of the World, 5th ed, vol. I, p515)Sequence Analysis, Protein: A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.Genetics, Population: The discipline studying genetic composition of populations and effects of factors such as GENETIC SELECTION, population size, MUTATION, migration, and GENETIC DRIFT on the frequencies of various GENOTYPES and PHENOTYPES using a variety of GENETIC TECHNIQUES.Hymenoptera: An extensive order of highly specialized insects including bees, wasps, and ants.Lagomorpha: An order of small mammals comprising two families, Ochotonidae (pikas) and Leporidae (RABBITS and HARES). Head and body length ranges from about 125 mm to 750 mm. Hares and rabbits have a short tail, and the pikas lack a tail. Rabbits are born furless and with both eyes and ears closed. HARES are born fully haired with eyes and ears open. All are vegetarians. (From Nowak, Walker's Mammals of the World, 5th ed, p539-41)Annelida: A phylum of metazoan invertebrates comprising the segmented worms, and including marine annelids (POLYCHAETA), freshwater annelids, earthworms (OLIGOCHAETA), and LEECHES. Only the leeches are of medical interest. (Dorland, 27th ed)Bacterial Proteins: Proteins found in any species of bacterium.Dinoflagellida: Flagellate EUKARYOTES, found mainly in the oceans. They are characterized by the presence of transverse and longitudinal flagella which propel the organisms in a rotating manner through the water. Dinoflagellida were formerly members of the class Phytomastigophorea under the old five kingdom paradigm.AfricaGenetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Selection, Genetic: Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.Porifera: The phylum of sponges which are sessile, suspension-feeding, multicellular animals that utilize flagellated cells called choanocytes to circulate water. Most are hermaphroditic. They are probably an early evolutionary side branch that gave rise to no other group of animals. Except for about 150 freshwater species, sponges are marine animals. They are a source of ALKALOIDS; STEROLS; and other complex molecules useful in medicine and biological research.North AmericaMarkov Chains: A stochastic process such that the conditional probability distribution for a state at any future instant, given the present state, is unaffected by any additional knowledge of the past history of the system.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Ecology: The branch of science concerned with the interrelationship of organisms and their ENVIRONMENT, especially as manifested by natural cycles and rhythms, community development and structure, interactions between different kinds of organisms, geographic distributions, and population alterations. (Webster's, 3d ed)Viridiplantae: A monophyletic group of green plants that includes all land plants (EMBRYOPHYTA) and all green algae (CHLOROPHYTA and STREPTOPHYTA).Wasps: Any of numerous winged hymenopterous insects of social as well as solitary habits and having formidable stings.Americas: The general name for NORTH AMERICA; CENTRAL AMERICA; and SOUTH AMERICA unspecified or combined.Platyrrhini: An infraorder of New World monkeys, comprised of the families AOTIDAE; ATELIDAE; CEBIDAE; and PITHECIIDAE. They are found exclusively in the Americas.DNA, Protozoan: Deoxyribonucleic acid that makes up the genetic material of protozoa.Programming, Linear: A technique of operations research for solving certain kinds of problems involving many variables where a best value or set of best values is to be found. It is most likely to be feasible when the quantity to be optimized, sometimes called the objective function, can be stated as a mathematical expression in terms of the various activities within the system, and when this expression is simply proportional to the measure of the activities, i.e., is linear, and when all the restrictions are also linear. It is different from computer programming, although problems using linear programming techniques may be programmed on a computer.Moles: Any of numerous burrowing mammals found in temperate regions and having minute eyes often covered with skin.Beetles: INSECTS of the order Coleoptera, containing over 350,000 species in 150 families. They possess hard bodies and their mouthparts are adapted for chewing.Genome, Chloroplast: The genetic complement of CHLOROPLASTS as represented in their DNA.Musaceae: A plant family of the order ZINGIBERALES, subclass Zingiberidae, class Liliopsida best known for banana (MUSA). The slender false trunk, formed by leaf sheaths of the spirally arranged leaves, may rise to 15 meters (50 feet). There is a crown of large leaves at the top.Dolphins: Mammals of the families Delphinidae (ocean dolphins), Iniidae, Lipotidae, Pontoporiidae, and Platanistidae (all river dolphins). Among the most well-known species are the BOTTLE-NOSED DOLPHIN and the KILLER WHALE (a dolphin). The common name dolphin is applied to small cetaceans having a beaklike snout and a slender, streamlined body, whereas PORPOISES are small cetaceans with a blunt snout and rather stocky body. (From Walker's Mammals of the World, 5th ed, pp978-9)Host-Parasite Interactions: The relationship between an invertebrate and another organism (the host), one of which lives at the expense of the other. Traditionally excluded from definition of parasites are pathogenic BACTERIA; FUNGI; VIRUSES; and PLANTS; though they may live parasitically.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)

*  Filosofía, especie y sistemática
structure of the Phylogeny of West Nile Virus WNV: Does it shape ... Host structure of the Phylogeny of West Nile Virus WNV: Does it shape the spatiotemporal structure. Methods Sequence Data: All the available sequences of complete genome of WNV, with collection times, and geographic locations 453 sequences, from 25 countries, and 79 hosts species were retrieved from GenBank. Phylogeny inferred using a Maximum likelihood analysis of 53 sequences. Phylogeny with Host structure for WNV. Just Testudines present a different resutl, where the non-nuclear and nuclear partitions had the lowest values Fig. Estimating Evolutionary Rates and Times to the last Common Ancestor DEV-2, using partitions vs complete coding region. Several studies have been aimed at understanding the epidemiology of DENV, rates and dates of evolution, and selection pressure in its different genes and genotypes Rico-hesse Rico-hesse, 1990; Rico-Hesse et al., 1997; S. The objectives of this study were to infer the time to the Most recent commo...
http://elecsist.blogspot.com/
*  Achondroplasia & FGFR3 - Home
gene. Homology. Phylogeny. Motifs. Ontology. RNAi. Chemical ... Homology. Phylogeny. Domains. Protein Interactions....
http://joycegen677s10.weebly.com/
*  ExPASy: SIB Bioinformatics Resource Portal - Home
category: genomics phylogeny/evolution proteomics systems biology - ... systems biology. phylogeny/evolution. population genetics. ... , genomics, phylogeny, systems biology, population genetics, ... ExPASy: SIB Bioinformatics Resource Portal - Home. Background and reference. Overview. Disclaimer. Contact. Support. SIB Groups. Find resources Query all databases - Query within a category: genomics phylogeny/evolution proteomics systems biology - Query a specific database: Cellosaurus ENZYME EPD GPSDB HAMAP miROrtho MyHits OMA OpenFlu OrthoDB PROSITE Protein Spotlight Selectome STRING SWISS-2DPAGE SWISS-MODEL Repository SwissDock SwissLipids SwissVar UniProtKB VenomZone ViralZone World-2DPAGE Repository. search help. Protein. Population. Categories. proteomics. protein sequences and identification mass spectrometry and 2-DE data protein characterisation and function families, patterns and profiles post-translational modification protein structure protein-protein interaction similarity search/alignment gen...
http://expasy.org/?tab=blast
*  Sleep
• Taxonomy Phylogeny • Virus • White Sites • Diagrams Tables ... Companion Sites : Gray Sites • Abiogenesis & Evolution • Algorithms of Evolution • Cancer • Cell Biology • Chemistry of Life • Cyanobacteria • Enzymes • Evo Devo • Fat • Immunology • Mechanisms of Evolution • Molecular Biology • Origin of Life • Paleogeology • Refuting ID • Serial Endosymbiosis • Stromatolites • Taxonomy Phylogeny • Virus • White Sites • Diagrams Tables • Eubacteria Archaea • Molecule • Molecular Paths • Pathways • Photosynthesis • Black Sites • Endosymbiosis • Organics •. Companion Sites : Gray Sites • Abiogenesis & Evolution • Algorithms of Evolution • Cancer • Cell Biology • Chemistry of Life • Cyanobacteria • Enzymes • Evo Devo • Fat • Immunology • Mechanisms of Evolution • Molecular Biology • Origin of Life • Paleogeology • Refuting ID • Serial Endosymbiosis • Stromatolites • Taxonomy Phylogeny • Virus • White Sites • Diagrams Tables • Eubacteria Archaea • Molecule • Molecular Paths • Pathways • Photosynthesis • Black Sites...
http://hypo-somnia.blogspot.com/
*  % GC content and 16S phylogeny
GC content and 16S phylogeny. % GC content and 16S phylogeny Thomas ... GC content and 16S phylogeny Next message: % GC content and 16S phylogeny Messages sorted by:. On 2 Aug 1996,...
http://bio.net/bionet/mm/mol-evol/1996-August/004597.html
*  ExPASy: SIB Bioinformatics Resource Portal - Resources
category: genomics phylogeny/evolution proteomics systems biology - ... systems biology. phylogeny/evolution. population genetics. ... expasy sib bioinformatics resource portal resources home about background and reference overview disclaimer contact support sib groups find resources query all databases query within a category genomics phylogeny evolution proteomics systems biology query a specific database cellosaurus enzyme epd gpsdb hamap mirortho myhits oma openflu orthodb prosite protein spotlight selectome string swiss dpage swiss model repository swissdock swisslipids swissvar uniprotkb venomzone viralzone world dpage repository search help visual guidance dna rna protein cell organism population categories proteomics protein sequences and identification mass spectrometry and de data protein characterisation and function families patterns and profiles post translational modification protein structure protein protein interaction similarity search alignment genomics sequence alignment similarity sea...
http://expasy.org/resources/detail/OpenFlu
*  ExPASy: SIB Bioinformatics Resource Portal - Resources
category: genomics phylogeny/evolution proteomics systems biology - ... systems biology. phylogeny/evolution. population genetics....
http://expasy.org/resources/detail/FindPept
*  MBG: Photo Essays
books angiosperm phylogeny res botanica all databases ... mbg photo essays www mobot org research home search contact site map w tropicos quick search mo projects africa asia pacific mesoamerica north america south america floras general taxonomy photo essays training in latin america mo research wm l brown center bryology gis graduate studies research experiences for undergraduates imaging lab library mbg press publications climate change catalog fossil plants mo databases w most image index rare books angiosperm phylogeny res botanica all databases information what s new people at mo visitor s guide herbarium jobs fellowships symposium research links site map search photo essay photo essay photo essay home introduction outline photo gallery search view larger image k photographer unspecified photographer pl...
http://mobot.org/mobot/photoessays/photoessay.asp?fldrloc=gabon&imgorder=0104
*  MBG: Photo Essays
Books Angiosperm Phylogeny Res Botanica All Databases....
http://mobot.org/mobot/photoessays/photoessay.asp?fldrloc=gabon&imgorder=0125
*  Biology, 8th Edition. Campbell. 9780321543257. 0321543254 | BookRenter.com
of Life on Earth, Phylogeny and the Tree of Life, Bacteria and...
https://bookrenter.com/biology-8th-edition-campbell-0321543254-9780321543257
*  CH391L/S12/CH391L/S12/Ancestral Sequence Reconstruction - OpenWetWare
... CH391L/S12/CH391L/S12/Ancestral Sequence Reconstruction From OpenWetWare CH391L/S12 Revision as of 15:45, 13 February 2012 by Jared Ellefson Talk. 1 What is Ancestral Sequence Reconstruction. 1.1 Pipeline for Generating Ancestral Genes 1.1.1 Methods of Inferring Ancient Sequences 1.1.2 Gene Synthesis 1.1.3 Testing Ancestral Variants. 1.2 Examples of Ancestral Sequence Reconstructions 1.2.1 Evolution of Coral Pigments 1.2.2 Inferring the Paleoenvironment of ancient Earth. What is Ancestral Sequence Reconstruction. Sequence information Nucleic Acid and Protein from extant species can be used to infer the sequences of common ancestor species which can be synthesized and tested in the lab. Sequence Reconstruction Example. Sequences from extant species of the desired common ancestral gene and outgroup genes are aligned. The ancestral gene is inferred based on evolutionary models typically maximum parsimony or maximum likelihood. Ancestral genes are cloned and tested for function. Methods of Inferring Ancient ...
http://openwetware.org/index.php?title=CH391L/S12/CH391L/S12/Ancestral_Sequence_Reconstruction&oldid=583945
*  CH391L/S13/Ancestral Sequence Reconstruction - OpenWetWare
... Ancestral Sequence Reconstruction refers to the construction of hypothesized protein or DNA sequences belonging to a common ancestor of extant proteins or DNA. Sequence information Nucleic Acid and Protein from extant species can be used to infer the sequences of common ancestor species which can be synthesized and tested in the lab. The method was originally discussed by Pauling and Zuckerkandl in 1963 cite Pauling /cite, almost 30 years before the theory was experimentally tested. Ancestral Sequence Reconstruction refers to the construction of hypothesized protein or DNA sequences belonging to a common ancestor of extant proteins or DNA. Sequence information Nucleic Acid and Protein from extant species can be used to infer the sequences of common ancestor species which can be synthesized and tested in the lab. The method was originally discussed by Pauling and Zuckerkandl in 1963 cite Pauling /cite, almost 30 years before the theory was experimentally tested. ==Pipeline for Generating Ancestral Genes==...
http://openwetware.org/index.php?title=CH391L/S13/Ancestral_Sequence_Reconstruction&diff=677463&oldid=677462
*  CH391L/S13/Ancestral Sequence Reconstruction - OpenWetWare
... CH391L/S13/Ancestral Sequence Reconstruction From OpenWetWare Difference between revisions Jump to: navigation, search Revision as of 19:53, 24 February 2013 view source Aurko Dasgupta Talk. contribs → Evolution of Coral Pigments ← Previous diff. Revision as of 19:55, 24 February 2013 view source Aurko Dasgupta Talk. contribs → Evolution of Coral Pigments Next diff →. Line 30:. Line 30:. One example of ancestral sequence reconstruction was done by the Matz group currently residing at the University of Texas at Austin. Fluorescent proteins from related coral species had wavelengths corresponding to Cyan, Green, and Red cite #Ugalde /cite. The details of the evolution of fluorescent color in the GFP superfamily was not fully understand. That is, what fluorescent spectra did the common ancestors of the modern corals have. One example of ancestral sequence reconstruction was done by the Matz group currently residing at the University of Texas at Austin. Fluorescent proteins from related coral species had wav...
http://openwetware.org/index.php?title=CH391L/S13/Ancestral_Sequence_Reconstruction&diff=678933&oldid=678932
*  Branching order of bacterial phyla (Gupta, 2001)
branching order of bacterial phyla gupta branching order of bacterial phyla gupta bacterial phyla there are several models of the branching order of bacterial phyla one of these was proposed in by gupta based on conserved indels or protein termed protein signatures an alternative approach to molecular phylogeny some problematic exceptions and conflicts are present to these conserved indels however they are in agreement with several groupings of classes and phyla one feature of the cladogram obtained with this method is the clustering of cell wall morphology with some exceptions from monoderms to transitional diderms to traditional diderms in the cladogram below yellow pseudopeptidoglycan monoderms gram variable red thick peptidoglycan monoderms gram positive blue thin peptidoglycan diderms gram negative green atypical see note in parethesis cladex style width auto bar gold archaea cladex bar crimson firmicutes cladex bar crimson actinobacteria see also branching order of bacterial phyla woese branching order ...
https://en.wikipedia.org/wiki/Branching_order_of_bacterial_phyla_(Gupta,_2001)
*  CH391L/S13/Ancestral Sequence Reconstruction - OpenWetWare
Fluorescent proteins from related coral species had wavelengths corresponding to Cyan, Green, and Red. That is, what fluorescent spectra did the common ancestors of the modern corals have. Sequences for the common ancestor nodes were synthesized and tested for their activity. The common ancestor to all the superfamily had a green emission peak. The more recent common ancestor of Green/Red had two emission peaks; a strong green peak and a smaller red peak. Fluorescent proteins from related coral species had wavelengths corresponding to Cyan, Green, and Red. That is, what fluorescent spectra did the common ancestors of the modern corals have. Sequences for the common ancestor nodes were synthesized and tested for their activity. The common ancestor to all the superfamily had a green emission peak. The more recent common ancestor of Green/Red had two emission peaks; a strong green peak and a smaller red peak. 1.2 Examples of Ancestral Sequence Reconstructions 1.2.1 Evolution of Coral Pigments 1.2.2 Inferring the...
http://openwetware.org/index.php?title=CH391L/S13/Ancestral_Sequence_Reconstruction&diff=678913&oldid=678912
*  The FASTML Server - Server for computing Maximum Likelihood ancestral sequence reconstruction
the fastml server server for computing maximum likelihood ancestral sequence reconstruction home overview gallery source code citing credits old version the fastml server server for computing maximum likelihood ancestral sequence reconstruction type your multiple sequence alignment msa fasta format only or upload your multiple sequence alignment msa file sequences type amino acids nucleotides codons type your phylogenetic tree optional newick format only or upload phylogenetic tree file newick format only model of substitution jtt default lg mtrev for mitochondrial proteins cprev for chloroplasts proteins wag dayhoff jc model jukes and cantor t model tamura hky model hasegawa kishino and yano gtr generalised time reversible yang for codon sequences empiricodon for codon sequences please enter your email address optional your email address will be used to update you the moment the results are ready load an example advanced options phylogenetic tree method maximum likelihood ml neighbor joining optimize branch ...
http://fastml.tau.ac.il/
*  Comparison of Protein Sequences: BLAST searching and Phylogenetic Tree Construction
... Inquiry-based Integrated Instructional Units Comparison of Protein Sequences: BLAST searching and Phylogenetic Tree Construction. It accompanies several weeks of wet lab work in which students clone cDNAs encoding Cytochrome P450 1A CYP1A from animals primarily fish collected locally and exposed to pollution compounds that induce expression of the enzyme. In this exercise, students perform BLAST searches of reported CYP1A sequences and construct phylogenetic trees using CYP1A amino acid sequences from various vertebrate species, especially those with multiple CYP1A paralogs. Thus, evolutionary analysis of CYP1A sequences from many species provides an opportunity to explore the number and timing of gene duplications during vertebrate evolution. Three short readings about gene duplication in evolution and phylogenetic analysis are provided at least one week prior to class. These readings complement earlier readings that specifically concern the cloning and evolutionary analysis of CYP1A genes in fish. Mate...
http://serc.carleton.edu/genomics/units/19100.html
*  Talk:CH391L/S13/Ancestral Sequence Reconstruction - OpenWetWare
... Talk:CH391L/S13/Ancestral Sequence Reconstruction. From OpenWetWare. Talk:CH391L/S13 Revision as of 00:02, 24 February 2013 by Aurko Dasgupta Talk. contribs. diff ←Older revision. Current revision diff. Newer revision→ diff. Jump to: navigation, search. Gabriel Wu 16:59, 18 February 2013 EST : Remove the cost and methods of gene synthesis or just reference the dna assembly section we've already gone over. Expand the codon optimization section unless this fits better in somewhere else. Gabriel Wu 16:59, 18 February 2013 EST : How does Pauling's proposal for ancestral gene construction relate to the actual discovery of DNA structure. Benjamin Gilman 13:21, 21 February 2013 EST : The Pauling and Zuckerkandl paper came out when the only protein sequence information we had came from limited peptide sequencing methods like Edman degradation N-terminal sequencing. You might add something about the shift to using DNA or RNA sequences to infer protein sequence once techniques like Maxam-Gilbert and Sanger sequenc...
http://openwetware.org/index.php?title=Talk:CH391L/S13/Ancestral_Sequence_Reconstruction&direction=prev&oldid=678776
*  Ancestral reconstruction
'Ancestral Reconstruction' also known as 'Character Mapping' or 'Character Optimization' is a method in evolutionary biology by which one can attempt to understand the phenotypic and genetic states of organisms that lived millions of years ago. Maximum Parsimony. Maximum likelihood. They are: maximum parsimony, maximum likelihood, and the Bayesian Inference. Maximum parsimony is the method that came about first. Maximum likelihood accounts for what we know about the likelihood of various events, which is that they are not all equal. Maximum Parsimony. Maximum Parsimony. Maximum likelihood. The main difference between this and maximum parsimony is that the maximum likelihood test accounts for the fact that not all events are equally likely to happen. When this is the case, maximum parsimony may actually be more accurate because it is more willing to make large, unlikely leaps than maximum likelihood is. Maximum likelihood has been shown to be quite reliable in reconstructing character states however it does no...
https://en.wikipedia.org/wiki/Ancestral_reconstruction
*  Viral phylodynamics
... Due to the impact that transmission dynamics and selection can have on viral genetic variation, viral phylogenies can therefore be used to investigate important epidemiological, immunological, and evolutionary processes, such as epidemic spread,. Methods Coalescent theory and phylodynamics. Examples Phylodynamics of Influenza. Phylodynamics of HIV. The clustering of taxa on a viral phylogeny will be affected by host population structure see figure 2 Viruses within similar hosts, such as hosts that reside in the same geographic region, are expected to be more closely related genetically if transmission occurs more commonly between them. For example, an application to HIV sequences within infected hosts showed that viral substitution rates dropped to effectively zero following the initiation of antiretroviral drug therapy. If the population size N t changes over time, the coalescent rate \lambda n t will also be a function of time. derived this rate for a time-varying population size under the assumption o...
https://en.wikipedia.org/wiki/Viral_phylodynamics
*  Diagnostic characters from Consortium of mx users. - Encyclopedia of Life
... Diagnostic characters. 2011, by Lewis L. Deitz and Matthew S. Wallace. Add to a collection. Diagnostic characters. Distance from eye to base of forewing usually greater than half eye width exceptions: Deiroderes and many Nicomiinae. Pronotum usually produced posteriorly over scutellum exceptions: Endoiastinae, Nicomiinae, Deiroderes, Abelus, and Hemicentrus, often also with anterior, lateral, or dorsal projections. Forewings with vein M fused with Cu basally share common stem; exceptions: some Nicomia and some Smiliinae. Prothoracic trochanter and femur not fused. Male abdominal segment IX usually with lateral plates discrete from pygofer exceptions: fused to pygofer in few members of various tribes; lateral plates absent in Anchistrotus and some Stegaspidini. Female pygofer not strongly produced posteroventrally. Nymph with abdominal tergum IX forming sheath around segment X, anal opening dorsal or posterior. Latest updates. No one has provided updates yet. Learn how to contribute. Add a new comment. Yo...
http://eol.org/data_objects/12685167
*  Browse By Person: Phillips, Matthew | QUT ePrints
Browse By Person: Phillips, Matthew. Browse By Person: Phillips, Matthew Statistics dashboard. Review. Book Chapter Phillips, Matthew J. Penny, David 2010 Mammalian phylogeny., Phillips, Matthew J. PLoS ONE, 10 5, e0125723., Carrano, Matthew T. Systematic Biology. Phillips, Matthew J., Gibb, Gillian C. 2014 Molecular phylogeny, biogeography, and habitat preference evolution of marsupials. Molecular Biology and Evolution, 31 9, pp., Phillips, Matthew J. Phillips, Matthew J., Gibb, Gillian,. Bunce, Michael 2013 Inferring kangaroo phylogeny from incongruent nuclear and mitochondrial genes. PLoS ONE, 8 2, pp. Phillips, Matthew J. Current Biology, 23 14, R603-R605., Phillips, Matthew J. Molecular Phylogenetics and Evolution, 59 3, pp., Phillips, Matthew J. 2010 Evolutionary relationships and divergence times among the native rats of Australia. 2009 The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography. 2009 Accounting for calibration uncertainty in phylogenetic estimation of evo...
http://eprints.qut.edu.au/view/person/Phillips,_Matthew.html
*  Wiegmann Lab: Current Research
Insect Molecular Systematics at NCSU. phylogenetic relationships and testing hypotheses about the evolution and diversification of insects. A major component of these studies is uncovering patterns and processes of DNA sequence evolution and using these to improve interpretation of morphological and developmental evolutionary pathways. Molecular Phylogenetics of Diptera: FLYTREE - NSF - Assembling the Tree of Life project on Diptera a Collaborative Research Effort in Dipteran Phylogenetics. The need for new, large, comprehensive datasets for Diptera phylogeny motivates our collaborative, National Science Foundation funded, Assembling the Tree of Life ATOL project-- FLYTREE. Within this study, we are assembling multiple phylogenetic data sets to simultaneously assess dipteran phylogenetic relationships and the information content of specific character systems. For example, we will compare large by character data sets 1st tier; 45 taxa; 15-20 genes and mt genomes to those with increased numbers of taxa by taxa ...
http://www4.ncsu.edu/unity/users/b/bwiegman/public_html/labweb/currentresearch.html
*  Talk:CH391L/S13/DirectedProteinEvolution - OpenWetWare
Gabriel Wu Talk. *' ] 21:45, 21 February 2013 EST ':It would be nice if you added literature examples of Directed Evolution of Proteins for each approach as done in the Ancestral Sequence Reconstruction or take a similar approach. *' ] 21:45, 21 February 2013 EST ':It would be nice if you added literature examples of Directed Evolution of Proteins for each approach as done in the Ancestral Sequence Reconstruction or take a similar approach. + *' ] 15:33, 2 March 2013 EST ':It would be nice to put some numbers on the typical plasmid screening in 'E. + ****' ] 14:03, 4 March 2013 EST ': This is an interesting point. *' ] 04:13, 27 February 2013 EST ':I thought it'd be nice to have a section explaining fitness landscapes and moving through sequence space. *' ] 04:13, 27 February 2013 EST ':I thought it'd be nice to have a section explaining fitness landscapes and moving through sequence space. It's true that many times the selection will result in being trapped in a local optima, but other times the selection wi...
http://openwetware.org/index.php?title=Talk:CH391L/S13/DirectedProteinEvolution&diff=680636&oldid=680003
*  Systematics
thumb|400px|A comparison of phylogenetic and phenetic concepts Biological '''systematics''' is the study of the diversification of living forms, both past and present, and the relationships among living things through time. Phylogenetic trees of species and higher taxa are used to study the evolution of traits e.g., anatomical or molecular characteristics and the distribution of organisms biogeography. Systematics, in other words, is used to understand the evolutionary history of life on Earth. Definition and relation with taxonomy Taxonomic characters See also References Notes. Definition and relation with taxonomy. Europeans tend to use the terms "systematics" and "biosystematics" for the field of the study of biodiversity as a whole, whereas North Americans tend to use "taxonomy" more frequently. Taxonomic characters. Molecular characters. Immunological distance Electrophoretic differences Amino acid sequences of proteins DNA hybridization DNA and RNA sequences Restriction endonuclease analyses Other molec...
https://en.wikipedia.org/wiki/Systematics
*  Difference between revisions of "Molecular Systematics Spring 2014" - EEBedia
Difference between revisions of "Molecular Systematics Spring 2014" From EEBedia. Chris Simon. Chris Simon. :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lab%208.%20Kasey%20Pregler%20MiniPresentation%2012April12.pdf}}EEB 5350 Lab 8. Kasey Pregler MiniPresentation 12April12.pdf. :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lab%208.%20Kasey%20Pregler%20MiniPresentation%2012April12.pdf}}EEB 5350 Lab 8. Kasey Pregler MiniPresentation 12April12.pdf. Instructor: Chris Simon, Biopharm 305D, 6-4640, chris.simon@uconn.edu Graduate Assistant: Chris Owen, Biopharm 325A, christopher.l.owen@uconn.edu ; 6-3947. Readings: will be posted as PDF’s. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. Syllabus Molecular Systematics rev 28 Mar 12.pdf Assignment 1. How molecules evo...
http://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2012&diff=21831&oldid=21782
*  Molecular phylogenetics
'Molecular phylogenetics ' is the branch of phylogeny that analyses hereditary molecular differences, mainly in DNA sequences, to gain information on an organism's evolutionary relationships. History of molecular phylogenetics Techniques and applications Theoretical background Limitations of molecular systematics See also Notes and references Further reading External links. A comprehensive step-by-step protocol on constructing phylogenetic tree, including DNA/Amino Acid contiguous sequence assembly, multiple sequence alignment, model-test testing best-fitting substitution models and phylogeny reconstruction using Maximum Likelihood and Bayesian Inference, is available at Nature Protocol Bast, F. These have been replaced in recent times largely by DNA sequencing, which produces the exact sequences of nucleotides or 'bases' in either DNA or RNA segments extracted using different techniques. In a molecular systematic analysis, the haplotypes are determined for a defined area of genetic material ; a substantial s...
https://en.wikipedia.org/wiki/Molecular_phylogenetics
*  CH391L/S13/DNA Computing - OpenWetWare
... CH391L/S13/DNA Computing From OpenWetWare Difference between revisions Jump to: navigation, search Revision as of 11:55, 1 April 2013 view source Dwight Tyler Fields Talk. contribs m New page: Hello world. ← Previous diff. Revision as of 12:03, 1 April 2013 view source Dwight Tyler Fields Talk. contribs m Next diff →. Line 1:. Line 1:. - Hello world. + ] ]. + =Introduction=. + Ancestral Sequence Reconstruction refers to the construction of hypothesized protein or DNA sequences belonging to a common ancestor of extant proteins or DNA. It enables scientists to synthesize biomolecules from extinct organisms. Sequence information Nucleic Acid and Protein from extant species can be used to infer the sequences of common ancestor species which can be synthesized and tested in the lab. The method was originally discussed by Pauling and Zuckerkandl in 1963 cite Pauling /cite, almost 30 years before the theory was experimentally tested. + ]. + + ==Pipeline for Generating Ancestral Genes==. + # Sequences from extan...
http://openwetware.org/index.php?title=CH391L/S13/DNA_Computing&diff=687401&oldid=687389
*  Phylogenetic Classification ( Real World ) | Biology | CK-12 Foundation
Phylogenetic Classification Real World. Help. Help. You are viewing an older version of this Concept. Go to the latest version. Phylogenetic Classification. Practice Phylogenetic Classification Practice. 0% Practice Now. Evolution. Resources. Published. Cows Gone Wild. The "cows" you see are Aurochs Bos primigenius. They are the species of bovine that humans domesticated to form our modern day cows. Looking at the cave paintings of aurochs, you may get the sense that they were a bit different than our domesticated cattle. The characteristics which made aurochs successful in the wild were not the characteristics that humans thought were most useful. For example, packing on lots of meat may be a great trait in a cow for a cattle rancher, but if that meat hampers mobility, then it can make a cow an easy target to predators. This is one of the differences between artificial selection and natural selection. However, it does not take 600 years for noticeable changes to appear in bred species once the artificial sel...
http://ck12.org/biology/Phylogenetic-Classification/rwa/21st-Century-Auroch/r8/
*  PCA and clustering reveal alternate mtDNA phylogeny of N and M clades. | Broad Institute of MIT and
PCA and clustering reveal alternate mtDNA phylogeny of N and M clades. Broad Institute of MIT and Harvard. Partnerships Philanthropy Careers Contact Us. What is Broad. Our Approach Areas of Focus History Leadership Who is Broad Partner Institutions Artist-in-Residence Media Center. Press Room News from the Broad Photos for Journalists Spotlight: Ebola Spotlight: CRISPR BroadMinded Blog Video Library For the Scientific Community. Scientific Publications Science Data Software. Scientific Publications Science Data Software. Home. News & Publications:Scientific Publications PCA and clustering reveal alternate mtDNA phylogeny of N and M clades. Recent Broad Publications Inherited CHST11/MIR3922 deletion is associated with a novel recessive syndrome presenting with skeletal malformation and malignant lymphoproliferative disease. Read More / View Supplemental Materials Ferritinophagy via NCOA4 is required for erythropoiesis and is regulated by iron dependent HERC2-mediated proteolysis. Read More / View Supplemental ...
https://broadinstitute.org/publications/broad3822
*  Phylogenomics
It is a group of techniques within the larger fields of phylogenetics and genomics. Phylogenomics draws information by comparing entire genomes, or at least large portions of genomes. 1 Phylogenetics compares and analyzes the sequences of single genes, or a small number of genes, as well as many other types of data. Prediction of gene function Establishment and clarification of evolutionary relationships Gene family evolution Prediction and retracing lateral gene transfer. Prediction of Gene Function Prediction and Retracing Lateral Gene Transfer Gene family evolution Establishment of Evolutionary Relationships Databases See also References. Before the use of phylogenomic techniques, predicting gene function was done primarily by comparing the gene sequence with the sequences of genes with known functions. 3 This prediction was based on the fact that this organism has a gene for which the sequence is highly similar to genes from other species in the "MutS" gene family which included many known to be involved ...
https://en.wikipedia.org/wiki/Phylogenomics
*  Wikiomics:RNA phylogenetics - OpenWetWare
... Wikiomics:RNA phylogenetics From OpenWetWare Difference between revisions Jump to: navigation, search Revision as of 17:04, 3 March 2008 view source Torsten Waldminghaus Talk. contribs added tags ← Previous diff. Current revision 05:34, 20 October 2009 view source Albert Vilella Talk. contribs adding rnasalsa. One intermediate revision not shown. Line 16:. Line 16:. * Bayesian Inference of Phylogeny. Allows secondary structure models. * Bayesian Inference of Phylogeny. Allows secondary structure models. * Designed specifically for use with RNA sequences that have a conserved secondary structure, e.g., rRNA and tRNA. Substitution models of sequence evolution that consider pairs of sites rather than single sites are implemented in this package along with standard nucleotides substitution models used nowadays. When a RNA molecule with a secondary structure is used in conjunction with a RNA substitution model, PHASE requires a structure-based alignment of the sequences with the consensus secondary structure ...
http://openwetware.org/index.php?title=Wikiomics:RNA_phylogenetics&diff=360520&oldid=189099
*  Polyphyly
Image:Monophyly, paraphyly, polyphyly.png File:Phylogenetic-Groups.svg|thumbnail|300px|Phylogenetic groups: A monophyletic taxon in yellow, the group of "reptiles and birds" contains a common ancestor and all of its descendants. A paraphyletic taxon in cyan, the reptiles contains its most recent common ancestor, but does not contain all the descendants of that ancestor. A polyphyletic in red, the group of all warm-blooded animals taxon does not contain the most recent common ancestor of all its members. A 'polyphyletic' Greek for "of many races" group is characterized by one or more homoplasies : phenotype s which have converged or reverted so as to appear to be the same but which have not been inherited from common ancestors. For example, warm-bloodedness evolved separately in the ancestors of mammals and the ancestors of birds 1. Researchers concerned more with ecology than with systematics may take polyphyletic groups as legitimate subject matter; the similarities in activity within the fungus group ' Alte...
https://en.wikipedia.org/wiki/Polyphyly
*  Difference between revisions of "Molecular Systematics Spring 2014" - EEBedia
Chris Simon. Chris Simon. :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB%205350%20Lab%209.%20Minipresentation%20RT-PCR%20Brigette.pdf}}EEB 5350 Lab 9. Minipresentation RT-PCR Brigette.pdf. :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB%205350%20Lab%209.%20Minipresentation%20RT-PCR%20Brigette.pdf}}EEB 5350 Lab 9. Minipresentation RT-PCR Brigette.pdf. Combining Data/Comparing Trees. + + :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Comparing%20Trees%20Combining%20Data%20Readings%202012.pdf}}Comparing Trees Combining Data Readings 2012.pdf. + + Reading for next week: :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Simon%2C%20Buckley%2C%20Frati%2C%20Stewart%2C%20Beckenbach%202006%20AREES%20%26%20supplement.pdf}}Simon, Buckley, Frati, Stewart, Beckenbach 2006 AREES supplement.pdf. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, ...
http://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2012&diff=21847&oldid=21846
*  Darwin's Evolutionary Tree 'Annihilated' | The Institute for Creation Research
Darwin s Evolutionary Tree Annihilated. Timely news related to creation and evolution. Life Sciences. Problems with Evolution. Evidence for Creation. Evidence for Truth. Evidence from Science. Apologetics Articles. ICR Store. Darwin's Evolutionary Tree 'Annihilated' by Brian Thomas, M.S. * Resources. Life Sciences Resources. Problems with Evolution. In 1837, Charles Darwin drew his first evolutionary tree in his B notebook, with the words I think scrawled above it, to illustrate his idea that all of today s species arose from a single common ancestor. But the poor fit of gene sequence data is forcing scientists to abandon the tree. A non-Darwinian evolutionary view has been offered, but this proposition is actually just the old Hopeful Monster with a twist. 3 Darwin s tree illustrated a long macroevolutionary past that never happened. 4 Finally, evolutionary biologists seem to be catching up with creation biologists. 5 Michael Syvanen, co-editor of Horizontal Gene Transfer 1998 and a medical biochemist at the...
http://icr.org/articles/view/4404/295/
*  Phylogenetic profiling
... 'Phylogenetic profiling' is a bioinformatics technique in which the joint presence or joint absence of two traits across large numbers of species is used to infer a meaningful biological connection, such as involvement of two different proteins in the same biological pathway. Along with examination of conserved synteny, conserved operon structure, or "Rosetta Stone" domain fusions, comparing phylogenetic profiles is a designated a "post-homology" technique, in that the computation essential to this method begins after it is determined which proteins are homologous to which. A number of these techniques were developed by David Eisenberg and colleagues; phylogenetic profile comparison was introduced in 1999 by Pellegrini, 'et al.' Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. Method Theory Advances and Challenges Notes. For a given protein family, its presence or absence in each genome in the original formulation is represented by 1 present and 0 absent. The large number of complete genom...
https://en.wikipedia.org/wiki/Phylogenetic_profiling
*  Structural Biochemistry/Analyzing protein structure and function using ancestral gene reconstruction
... - Wikibooks, open books for an open world. Structural Biochemistry/Analyzing protein structure and function using ancestral gene reconstruction. 1 Analyzing protein structure and function using ancestral gene reconstruction. Analyzing protein structure and function using ancestral gene reconstruction. Learning how protein sequence determines structure and function as well as learning the processes that generated the diverse structures and functions of extant proteins requires knowledge of the distribution of structures and functions through the multidimensional space of possible protein sequences. The outcomes of that massive experiment are preserved in the sequences, structures, and functions of modern-day protein families. Evolutionary analysis of these families can provide key insights into the nature of protein sequence space and the determinants of protein structure and function. Horizontal and Vertical Analysis. One way to study protein families is to identify candidate amino acid differences betwe...
https://en.wikibooks.org/wiki/Structural_Biochemistry/Analyzing_protein_structure_and_function_using_ancestral_gene_reconstruction
*  Patrocladogram
2 " and is used exclusively to determine the amount of divergence of a characteristic from a common ancestor. This means that cladistic and patristic distances are combined to construct a new tree using various phenetic algorithms. 3 The purpose of the patrocladogram in biological classification is to form a hypothesis about which evolutionary processes are actually involved before making a taxonomic decision. 4 Patrocladograms are based on biostatistics that include but are not limited to: parsimony, distance matrix, likelihood method s, and Bayesian probability. Some examples of genomically related data that can be used as inputs for these methods are: molecular sequences, whole genome sequences, gene frequencies, restriction site s, distance matrices, unique characters, mutations such as SNPs, and mitochondrial genome data. Cautions with patrocladogram usage Programs for patrocladogram analysis PATRISTIC. RAMI. Further reading References External links. Cautions with patrocladogram usage. Patrocladograms a...
https://en.wikipedia.org/wiki/Patrocladogram
*  SMART: DUF1866 domain taxonomic distribution
smart duf domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with duf domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing duf domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=DUF1866
*  SMART: DUF3700 domain taxonomic distribution
smart duf domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with duf domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing duf domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=DUF3700
*  SMART: PTPc motif domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with PTPc motif domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing PTPc motif domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=PTPc_motif
*  SMART: HOX domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with HOX domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing HOX domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=HOX
*  SMART: Citrate ly lig domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with Citrate ly lig domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing Citrate ly lig domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Citrate_ly_lig
*  SMART: Catalase domain taxonomic distribution
smart catalase domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with catalase domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing catalase domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Catalase
*  SMART: LRR RI domain taxonomic distribution
smart lrr ri domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with lrr ri domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing lrr ri domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=LRR_RI
*  SMART: Fib alpha domain taxonomic distribution
smart fib alpha domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with fib alpha domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing fib alpha domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Fib_alpha
*  SMART: Frataxin Cyay domain taxonomic distribution
smart frataxin cyay domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with frataxin cyay domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing frataxin cyay domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Frataxin_Cyay
*  SMART: Integrin B tail domain taxonomic distribution
smart integrin b tail domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with integrin b tail domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing integrin b tail domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Integrin_B_tail
*  SMART: BMC domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with BMC domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing BMC domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=BMC
*  SMART: GA domain taxonomic distribution
smart ga domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with ga domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing ga domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=GA
*  SMART: ELK domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with ELK domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing ELK domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=ELK
*  SMART: SEC14 domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with SEC14 domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing SEC14 domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=SEC14
*  SMART: CP12 domain taxonomic distribution
smart cp domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with cp domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing cp domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=CP12
*  SMART: NH domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with NH domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing NH domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=NH
*  SMART: DM13 domain taxonomic distribution
smart dm domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with dm domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing dm domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=DM13
*  SMART: LY domain taxonomic distribution
smart ly domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with ly domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing ly domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=LY
*  SMART: zf-AD domain taxonomic distribution
smart zf ad domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with zf ad domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing zf ad domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=zf-AD
*  SMART: AWS domain taxonomic distribution
smart aws domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with aws domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing aws domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=AWS
*  SMART: Amelin domain taxonomic distribution
smart amelin domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with amelin domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing amelin domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Amelin
*  SMART: Ami 3 domain taxonomic distribution
smart ami domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with ami domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing ami domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Ami_3
*  SMART: C2 domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with C2 domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing C2 domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=C2
*  SMART: CLH domain taxonomic distribution
smart clh domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with clh domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing clh domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=CLH
*  SMART: CVNH domain taxonomic distribution
smart cvnh domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with cvnh domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing cvnh domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=CVNH
*  SMART: Cache 2 domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with Cache 2 domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing Cache 2 domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Cache_2
*  SMART: ChSh domain taxonomic distribution
smart chsh domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with chsh domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing chsh domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=ChSh
*  SMART: DAX domain taxonomic distribution
smart dax domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with dax domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing dax domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=DAX
*  SMART: DEFSN domain taxonomic distribution
smart defsn domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with defsn domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing defsn domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=DEFSN
*  SMART: DSHCT domain taxonomic distribution
smart dshct domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with dshct domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing dshct domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=DSHCT
*  SMART: DSPc domain taxonomic distribution
smart dspc domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with dspc domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing dspc domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=DSPc
*  SMART: EPEND domain taxonomic distribution
smart epend domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with epend domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing epend domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=EPEND
*  SMART: FBG domain taxonomic distribution
smart fbg domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with fbg domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing fbg domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=FBG
*  SMART: GPS domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with GPS domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing GPS domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=GPS
*  SMART: GYR domain taxonomic distribution
smart gyr domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with gyr domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing gyr domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=GYR
*  SMART: HALZ domain taxonomic distribution
smart halz domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with halz domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing halz domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=HALZ
*  SMART: LNS2 domain taxonomic distribution
smart lns domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with lns domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing lns domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=LNS2
*  SMART: MltA domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with MltA domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing MltA domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=MltA
*  SMART: MutL C domain taxonomic distribution
smart mutl c domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with mutl c domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing mutl c domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=MutL_C
*  SMART: NMU domain taxonomic distribution
smart nmu domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with nmu domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing nmu domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=NMU
*  SMART: NRF domain taxonomic distribution
smart nrf domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with nrf domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing nrf domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=NRF
*  SMART: NurA domain taxonomic distribution
smart nura domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with nura domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing nura domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=NurA
*  SMART: PA14 domain taxonomic distribution
smart pa domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with pa domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing pa domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=PA14
*  SMART: PMEI domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with PMEI domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing PMEI domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=PMEI
*  SMART: ParB domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with ParB domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing ParB domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=ParB
*  SMART: RPEL domain taxonomic distribution
smart rpel domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with rpel domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing rpel domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=RPEL
*  SMART: RasGAP domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with RasGAP domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing RasGAP domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=RasGAP
*  SMART: SPK domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with SPK domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing SPK domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic....
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=SPK
*  SMART: SPRY domain taxonomic distribution
smart spry domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with spry domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing spry domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=SPRY
*  SMART: VRR NUC domain taxonomic distribution
smart vrr nuc domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with vrr nuc domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing vrr nuc domain in the selected taxonomic class embl send comments to ivica letunic...
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=VRR_NUC
*  Treefinder
{{Infobox Software name = TreeFinder developer = Gangolf Jobb latest release version = march2011 latest release date =. A platform-independent graphical environment integrates a standard suite of analyses: phylogeny reconstruction, bootstrap analysis, model selection, hypothesis testing, tree calibration, manipulation of trees and sequence data. Result trees are displayed and can then be saved as a reconstruction report, which may serve as an input for further analysis, for example hypothesis testing. The report contains all information about the tree and the models used. The software supports a broad collection of models of sequence evolution. The June 2008 release implements 7 models of nucleotide substitution HKY, TN, J1, J2, J3 = TIM, TVM, GTR, 14 empirical models of amino acid substitution BLOSUM, cpREV, Dayhoff, JTT, LG, mtArt, mtMam, mtREV, PMB, rtREV, betHIV, witHIV, VT, WAG, 4 substitution models of structured rRNA bactRNA, eukRNA, euk23RNA, mitoRNA, the 6-state "Dayhoff Groups" protein model DG, 2-s...
https://en.wikipedia.org/wiki/Treefinder
*  Human mitochondrial molecular clock
... Estimating based on AMH archaeology Estimating based on CHLCA Early, HVR, sequence-based methods Coding region sequence based methods Inter-comparing rates and studies Notes Footnotes References. The rate at which mutations accumulate in coding and non-coding region s of the genome also differs as mutations in the coding region are subject to purifying selection. For this reason, some studies avoid coding region or synonymous mutations when calibrating the molecular clock. Pedigree methods estimate the mutation rate by comparing the mtDNA sequences of a sample of parent/offspring pairs or analyzing mtDNA sequences of individuals from a deep-rooted genealogy. Phylogeny based methods are estimated by first reconstructing the haplotype of the most recent common ancestor MRCA of a sample of two or more genetic lineages. The human mutation rate is usually estimated by comparing the sequences of modern humans and chimpanzees and then reconstructing the ancestral haplotype of the chimpanzee-human common ancesto...
https://en.wikipedia.org/wiki/Human_mitochondrial_molecular_clock
*  blogzilly: In Light of Recent Events
... In Light of Recent Events. Unfortunately, the post I wanted to get to today will have to wait for another time. This happens when you have a youngster with multiple disabilities, one of them related to aggressive behaviors, in the public school system, and you get phone calls that suck you into it's vortex away from your job and away from other things you may have going on. I have a LOT to catch you people up on. Today. Carter was home sick, time slipped out of my hands, and by the time I had to watch the kids at night Jen works some late night shifts now ...well, I never am comfortable in the shower if Bennett is here without other supervision. Like putting on a nice worn-in old coat and finding a crisp $50 bill in it from the winter before. I can already see I am going to feel much more relaxed this year But yeah...we still have major communication delays and stuff like that out the wazoo. In fact, even though a lot of stuff has changed in a year. Let's see...I've covered being smelly and unwashed, boo...
http://blogzilly.blogspot.com/2014/02/in-light-of-recent-events.html
*  Debian -- Details of package phyml in wheezy
... / Packages / wheezy oldstable / science / phyml. package names descriptions source package names package contents. all options. Links for phyml. Homepage Similar packages: fasttree. PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework the non-parametric bootstrap and the approximate likelihood ratio test. PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be analyzed. In practice however, the amount ...
https://packages.debian.org/nl/wheezy/ia64/phyml
*  Systematics of Green Coccoid Algae: the Genus Bracteacoccus - EEBedia
... Systematics of Green Coccoid Algae: the Genus Bracteacoccus From EEBedia Revision as of 15:59, 29 September 2008 by KarolinaFucikova. diff ← Older revision. Latest revision diff. Newer revision → diff. Jump to: navigation, search Karolina Fučíková L. Green algae Chlorophyta are a morphologically heterogeneous group that is undergoing considerable revisions at present. Especially in coccoid genera, there have been striking cases of polyphyly, when species originally placed in one genus were shown to belong to up to three different classes. The coccoid chlorophycean genus Bracteacoccus Tereg was until recently considered monophyletic, but with the advent of new molecular data, it no longer appears as such. The goal of my project is to monograph the genus Bracteacoccus. I collect 18S ribosomal DNA sequences nuclear gene as well as rbcL sequences chloroplast, protein-coding gene. Like other coccoid genera, Bracteacoccus has very simple morphology and therefore few characters to be scored. Transmission electr...
http://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_of_Green_Coccoid_Algae:_the_Genus_Bracteacoccus&oldid=8372
*  Systematics of Green Coccoid Algae: the Genus Bracteacoccus - EEBedia
... Systematics of Green Coccoid Algae: the Genus Bracteacoccus From EEBedia Revision as of 22:09, 27 April 2008 by KarolinaFucikova. Talk. contribs. diff ← Older revision. Latest revision diff. Newer revision → diff. Jump to: navigation, search Karolina Fucikova L. Lewis Lab. Green algae Chlorophyta are a morphologically heterogeneous group that is undergoing considerable revisions at present. Especially in coccoid genera, there have been striking cases of polyphyly, when species originally placed in one genus were shown to belong to up to three different classes. The coccoid chlorophycean genus Bracteacoccus Tereg was until recently considered monophyletic, but with the advent of new molecular data, it no longer appears as such. The goal of my project is to monograph the genus Bracteacoccus. I collect 18S ribosomal DNA sequences nuclear gene as well as rbcL sequences chloroplast, protein-coding gene. Phylogeny obtained from the sequence data can be subsequently used as a starting point for further research...
http://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_of_Green_Coccoid_Algae:_the_Genus_Bracteacoccus&oldid=6391
*  The Tree of Life: Now this is my kind of meeting
4 days ago from Tweetie phylogenomics Andrew Roger at #CIFAR is talking about the origin and evolution of mitochondria and related organelles 4 days ago from TwitterFon phylogenomics Joel Dacks at #CIFAR is talking about evolution of eukaryotic membrane traffiicking how it is about "more than just eating" 4 days ago from TwitterFon JATetro @phylogenomics Will there be a proceedings or at least a review of the meeting. #CIFAR 4 days ago from Seesmic Desktop phylogenomics Tom Cavalier-Smith at #CIFAR is one of the few people who can really mix molecar phylogenetics and function/morphology for microbial euks 4 days ago from TwitterFon phylogenomics Listening to THE Tom Cavalier-Smith talking about eukaryotic evolution at #CIFAR - I don't always agree with him but he still rocks 4 days ago from TwitterFon phylogenomics Yan Boucher at #CIFAR is talking about "the life aquatic - vibrio an their mobile gene pool" - looking at lateral transfer recombination 4 days ago from TwitterFon matthewherper RT @phylogenomics A...
http://phylogenomics.blogspot.com/2009/06/now-this-is-my-kind-of-meeting.html
*  Predoc05 Practical Answers
No - and yes. These proteins cannot be homologous. Are there SM-like proteins found in Archaea. Good low P-values are reliable but actually there are many SM proteins, with weak P-values and still others that are not detected at all. So the P-values are not reliable for the more divergent but related sequences. Yes they are strong. They are all common domains. Are there structures for any of these domains. Yes, many have been found in kinase domains for example. Do you think this protein has especially many or few domains. There are many proteins with just a few domains but also many proteins with huge numbers of domains. This protein is made of only two kinds of domain - but has more than 50 of them. Exploring order/disorder with Globplot Questions and Answers Why does GlobPlot not slide a fixed window length over the sequences. But the graph indicates that these regions have mainly globular preference. These are all splendid proteins to explore with GlobPlot. Are there any annotated motifs. For the src CDK ...
http://embl.de/~seqanal/courses/predoc05/predoc05.answers.html
*  bernard SERIN - Member profile - Famille - MyHeritage
... You are not logged in Log in Sign up. You are currently not logged in as a member of MyHeritage. Log in or Sign up. Famille. You are not logged in Log in. Sign up. Site members Family tree. Family tree. Manage trees Photos. Family photos. Search photos Apps. MyHeritage for mobile. Family Tree Builder. Search all records. Birth, Marriage & Death. Census & Voter Lists. Family Trees. Immigration & Travel Hire a researcher. DNA tests. Members. bernard SERIN. Viewed this profile 0000236. bernard SERIN. bernard is a member of the site Famille. Other site memberships by number of visits Famille Caradec LeTessier Member, since June 23 2011. Ocio Costales Web Site Member, since Sep 3 2012. sylvie Web Site Member, since Nov 13 2012. Fradin Web Site Member, since Mar 2 2011. Family history Web Site Member, since July 16 2011. Boulanger Web Site Member, since Dec 19 2011. DENHAUT Web Site Member, since Apr 23 2012. DEMARZO Web Site Member, since Sep 4 2015. SALAFA Web Site Member, since July 18 2015. Bosse Web...
http://myheritage.com/member-46601113_74865261/bernard-serin
*  SC-500E Single Event Stopwatch
sc e single event stopwatch my account log in items view cart men s swim gear women s swim gear team swim gear kids swim gear swim equipment swim accessories clearance items team login shop by brand featured products search products many thanks jeannie your customer service is top notch i wouldn t hesitate to order from you again jorie centerville oh splashwear sc e silent and audible single event stopwatch sc e silent and audible single event stopwatch can be used error free by anyone for accurate results item robic our price quantity volume discounts available of items price product details one step timing for all events start stop reset operation second resolution to hours audible beep confirmation or silent operation water resistant to meters break away safety lanyard helps prevent accidents promotes safe use one year warranty lithium batter cr other items you may like oslo w dual stopwatch countdown timer robic sc w heat stress comfort index stopwatch robic sc w dual memory speed and chronograph stopwatc...
http://swimmerstuff.com/sc500e-single-event-stopwatch-14_1515_p.aspx
*  Tinton Falls, NJ Apartments for Rent - 64 Apartments | Rent.com®
Tinton Falls, NJ Apartments for Rent - 64 Apartments. Apartments for Rent in Tinton Falls, NJ Local Info 64 Properties. 333 Tinton Falls, NJ 07753 $1745 - $2205 1-3 Beds 1-2 Baths 732 481-2168 Check Availability. 216 Units 1-3 Beds 1-2 Baths View More Info Current Rent Specials. Sea Verge Long Branch, NJ 07740 $1430 - $3395 0-2 Beds 1-2 Baths 732 734-0157 Check Availability. 126 Units 0-2 Beds 1-2 Baths View More Info Current Rent Specials. 18 Long Branch, NJ 07740 $1400 - $4415 0-3 Beds 1-2 Baths 732 443-1255 Check Availability. 283 Units 0-3 Beds 1-2 Baths View More Info Current Rent Specials. 412 Units 1-2 Beds 1 Bath View More Info Current Rent Specials. 108 Units 1-2 Beds 1 Bath View More Info Current Rent Specials. 229 West Long Branch, NJ 07764 $1740 - $2665 1-3 Beds 1-2 Baths 732 603-1189 Check Availability. 2 Long Branch, NJ 07740 $1160 - $1585 1-2 Beds 1 Bath 732 963-0001 Check Availability. 8 West End, NJ 07740 $1190 - $1685 1-2 Beds 1 Bath 732 963-2988 Check Availability. Monmouth Beach Village Lo...
http://rent.com/new-jersey/tinton-falls-apartments/2-21664
*  Sequence data and cladistics
... agneta guillemot agneta guillemot at historia umu se tue may est previous message re dna from formalin fixed specimen next message sequence data and cladistics messages sorted by i have a question to systematicists concerning molecular sequences and it s application in cladistic analyses the question is as follows has anyone ever been able to prove anything in a true cladistic analysis with sequence data from proteins or dna i m not interested in talk about molecular clocks and what they are presumed to have proved concerning the relationships of different taxa only in true cladistics what i want to see with my own eyes are unique sequences in dna or proteins not single substitutions of an amino acid or a base pair shared by the taxa you want group together while the other candidates for inclusion into this group have the primitive sequence as determined by outgroup comparison to you who knows anything about this please include in your reply to this forum if it s not to much work a short list of articles...
http://bio.net/bionet/mm/mol-evol/1995-May/002776.html
*  .. Phylogenetic trees from 16S rRNA .. Two-dimensional clustering .. Concluding remarks .. Group wo
XML file. We have provided a template for this file, and shall add only a section defining which genomes to be compared. This will depend on who has finished the gene prediction and translation ;- Build the configuration This is done by the scell script make-bm-config.csh - feel free to examine it using less. The scripts simply checks who has finished the *.proteins.fsa file and then build the configuration file accordingly. csh make-bm-config.csh blastmatrix.head.xml > blastmatrix.xml less blastmatrix.xml Running blast matrix program Running the BLAST matrix program scales badly with the number of proteomes n 2 and therefor takes a long time to finish for all your genomes. Luckily the program features a caching system which enables it to reuse results from searches it has already performed. For those of you who are interrested, the program uses MD5 checksums of the input proteomes to keep track of the results - this is a very convinient way to keep track of changes in large data files. We have primed the cac...
http://cbs.dtu.dk/courses/thaiworkshop08/docs/m16.php?grp=stud111
*  PLOS ONE: Distinct Patterns of HIV-1 Evolution within Metastatic Tissues in Patients with Non-Hodgki
Article-Level Metrics. View. Sum of PLOS and PubMed Central page views and downloads. Open Access Peer-reviewed Research Article. Article. Similar results were found in both patients: 1 high-resolution phylogenetic analysis showed a significant degree of compartmentalization between lymphoma and non-lymphoma viral sub-populations while viral sub-populations from lymph nodes appeared to be intermixed within sequences from tumor and non-tumor tissues, 2 a 100-fold increase in the effective HIV population size in tumor versus non-tumor tissues was associated with the emergence of lymphadenopathy and aggressive metastatic ARL, and 3 HIV gene flow among lymph nodes, normal and metastatic tissues was non-random. Overall, the results clearly demonstrated that the HIV strains within tumor associated macrophages in both subjects belonged to a unique viral population that was phylogenetically distinct from the strains infecting macrophages and T cells in non-tumor tissues. To address this hypothesis, HIV-1 rate of evol...
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008153
*  human biology - Are homozygous carriers of the CCR5-Δ32 allele fully immune to all known strains of
... HIV. - Biology Stack Exchange. current community. chat blog. Biology. . Biology Meta. your communities. Sign up or log in to customize your list. more stack exchange communities. Stack Exchange. Inbox. Reputation and Badges. sign up log in tour. help. Tour Start here for a quick overview of the site. Help Center Detailed answers to any questions you might have. Meta Discuss the workings and policies of this site. Biology Questions. Tags. Users. Badges. Unanswered. Ask Question. Sign up. Biology Stack Exchange is a question and answer site for biology researchers, academics, and students. It's 100% free, no registration required. Are homozygous carriers of the CCR5-Δ32 allele fully immune to all known strains of HIV. up vote 10 down vote favorite. Or is there documented evidence of even one homozygous carrier contracting HIV and staying infected. human-biology genetics virology hiv share. improve this question. edited Jan 12 '13 at 11:20. Rory M 8,697. 5 34. 78. asked Feb 10 '12 at 19:02. mring 883. 4...
http://biology.stackexchange.com/questions/975/are-homozygous-carriers-of-the-ccr5-Δ32-allele-fully-immune-to-all-known-strains/1020
*  The Protein Family Tree
... . The Protein Family Tree How can the flood of human genomic data be gainfully employed. The first step is using sequence data to determine 3-D protein structure. But how can scientists wade efficiently through this massive information to solve hundreds of thousands of proteins that remain unsolved. A series of software tools, some of them developed at PSC, make it possible to search databases and classify proteins in family groups that reflect the evolutionary relationships that select for protein function. PSC and University of Pittsburgh scientists have exhaustively analyzed the relationships among a family of enzymes called aldehyde dehydrogenase. Found in nearly every living thing, ALDH in mammals protects the body from toxic compounds. In this graphical representation of the ALDH molecular structure top, right, colors represent amino-acid groups that are "highly conserved" - they remain essentially the same in nearly all species of the enzyme. The logic of evolution holds that conserved residues ar...
http://psc.edu/science/2001/highlights/the_protein_family_tree.html
*  Recently Active 'bioinformatics' Questions - Biology Stack Exchange
Recently Active 'bioinformatics' Questions - Biology Stack Exchange. current community. chat blog. Biology. . Biology Meta. your communities. Sign up or log in to customize your list. more stack exchange communities. Stack Exchange. Inbox. Reputation and Badges. sign up log in tour. help. Tour Start here for a quick overview of the site. Help Center Detailed answers to any questions you might have. Meta Discuss the workings and policies of this site. Biology Questions. Tags. Users. Badges. Unanswered. Ask Question. Tagged Questions info newest frequent votes active unanswered. Bioinformatics connects life sciences and quantitative sciences, typically involving the application of software and algorithms to solve computationally intensive questions, such as those in genomics, sequence analysis, and systems biology. Questions tagged Bioinformatics should have a direct ... learn more. top users. synonyms 1. 3 votes. 2 answers. 83 views. Do the bacterial species X, Y, Z code for proteins A, B, C. My PI has...
http://biology.stackexchange.com/questions/tagged/bioinformatics?sort=active&pageSize=15
*  Take The Which Lost Character Are You Test | OkCupid
Take The Which Lost Character Are You Test. OkCupid. OkCupid. Join the best free dating site on Earth. Sign in. Sign up. The Which Lost Character Are You Test Member Tests 0. Staff Tests 0. Test 0. Take this test. Danielle. You've been stuck on that damn island for so long you don't know what's going on anymore. Take The Which Lost Character Are You Test See more tests. If you don't, I will kill one of them. Oh, and Charlie, I will kill you last." You are Ethan Ro... Read more Danielle "You have three choices: run, hide or die." You are Danielle Rosseau, the French woman. You're not the most social person on the island, but you don't mind. As long as yo... Read more Locke "You're not going crazy, Jack. Crazy people don't think they're getting crazy. You are a good worker and p... Read more Claire "Don't talk to me about the baby. You are a very kind and caring person. It's gonna be a while before you're going to want to give me a piggy back ride." Dude, you are Hurley. You are a kind s... Read more Claire* "D...
http://okcupid.com/quizzy/results?quizzyid=5052228135609532493&resultid=4
*  TIGR03266
... . TIGRFAMs. JCVI Home. TIGRFAMs Home. Genome Properties. TIGRFAMs Home. TIGRFAMs Terms. TIGRFAMs Complete Listing. TIGRFAMs FTP site. TIGRFAMs Resources. TIGR03266 Seed Alignment. HMM Summary Page: TIGR03266. Accession. TIGR03266. Name. methan mark 1. Function. putative methanogenesis marker protein 1. Trusted Cutoff. 365.00. Domain Trusted Cutoff. 365.00. Noise Cutoff. 265.00. Domain Noise Cutoff. 265.00. Isology Type. hypoth equivalog. HMM Length. 376. Author. Haft DH. Entry Date. Jan 16 2007 4:43PM. Last Modified. May 9 2011 8:01PM. Comment. Members of this protein family represent a distinct clade among the larger set of proteins that belong to families TIGR00702 and PF02624. Proteins from this clade are found in genome sequence if and only if the species sequenced is one of the methanogens. All methanogens belong to the archaea; some but not all of those sequenced are hyperthermophiles. This protein family was detected by the method of partial phylogenetic profiling see Haft, et al., 2006. Reference...
http://jcvi.org/cgi-bin/tigrfams/HmmReportPage.cgi?acc=TIGR03266
*  SMART: DUF1220 domain annotation
... CHROMA format CLUSTALW format MSF format FASTA format PIR format. There are 2239 DUF1220 domains in 453 proteins in SMART's nrdb database. Click on the following links for more information. Evolution species in which this domain is found Taxonomic distribution of proteins containing DUF1220 domain. The complete taxonomic breakdown of all proteins with DUF1220 domain is also avaliable. Click on the protein counts, or double click on taxonomic names to display all proteins containing DUF1220 domain in the selected taxonomic class. Dumas L, Sikela JM DUF1220 domains, cognitive disease, and human brain evolution. 2009; 74 : 375-82 Display abstract We have established that human genome sequences encoding a novel protein domain, DUF1220, show a dramatically elevated copy number in the human lineage >200copies in humans vs. Copy-number variations CNVs in the 1q21.1 region, where mostDUF1220 sequences map, have now been implicated in numerous diseases associatedwith cognitive dysfunction, including autism, autis...
http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=DUF1220&BLAST=DUMMY
*  Bio-IT World
New studies of the bacterium that causes anthrax will involve “a lot more sequencing, phylogenetic context, and developing molecular signatures for strains,” says P. New phylogenetic trees could also provide better analytical tools for predicting the functions of unknown proteins. In new findings, Keim and colleagues at Los Alamos and TIGR have recently identified differences among several Ames samples. TIGR intends to sequence the genomes of as many as 14 anthrax strains from around the world, far more than have been sequenced for any other species. “What is needed is an archive containing a fair number of samples and a strategy for going from sequencing of multiple, whole genomes to finding regions containing highly specific molecular signatures,” White says. The Los Alamos group is developing a process for establishing such signatures in any pathogen based on a molecular taxonomic approach, which White describes as the “rational design of DNA signatures.” The development of such signatures for bacteria is ...
http://bio-itworld.com/archive/040702/anthrax/

Branching order of bacterial phyla (Gupta, 2001): There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved indels, however, they are in agreement with several groupings of classes and phyla.Molecular evolution: Molecular evolution is a change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes.DNA sequencer: A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine).Decoding methods: In coding theory, decoding is the process of translating received messages into codewords of a given code. There have been many common methods of mapping messages to codewords.Coles PhillipsHaplogroup L0 (mtDNA)CS-BLASTHyperparameter: In Bayesian statistics, a hyperparameter is a parameter of a prior distribution; the term is used to distinguish them from parameters of the model for the underlying system under analysis.Large ornamented Ediacaran microfossil: Large ornamented Ediacaran microfossils (LOEMs) are microscopic acritarchs, usually over 100 μm in diameter, which are common in sediments of the Ediacaran period, . They largely disappear from the Ediacaran fossil record before , roughly coeval with the origin of the Ediacara biota.Community Fingerprinting: Community fingerprinting refers to a set of molecular biology techniques that can be used to quickly profile the diversity of a microbial community. Rather than directly identifying or counting individual cells in an environmental sample, these techniques show how many variants of a gene are present.Amplified Ribosomal DNA Restriction Analysis: Amplified rDNA (Ribosomal DNA) Restriction Analysis is the extension of the technique of RFLP (restriction fragment length polymorphism) to the gene encoding the small (16s) ribosomal subunit of bacteria. The technique involves an enzymatic amplification using primers directed at the conserved regions at the ends of the 16s gene, followed by digestion using tetracutter Restriction enzymes.Genetic variation: right|thumbPhylogeography: Phylogeography is the study of the historical processes that may be responsible for the contemporary geographic distributions of individuals. This is accomplished by considering the geographic distribution of individuals in light of the patterns associated with a gene genealogy.NADH-QSymmetry element: A symmetry element is a point of reference about which symmetry operations can take place. In particular, symmetry elements can be centers of inversion, axes of rotation and mirror planes.Glossary of scientific names: A glossary of the meaning of scientific names of living things, viruses and prions .Horizontal gene transfer in evolutionAmborellaHealth geography: Health geography is the application of geographical information, perspectives, and methods to the study of health, disease, and health care.Bennettites: Bennettites refers to an extinct genus of the order Bennettitales.BrachiopodStromule: A stromule is a microscopic structure found in plant cells. Stromules (stroma-filled tubules) are highly dynamic structures extending from the surface of all plastid types, including proplastids, chloroplasts, etioplasts, leucoplasts, amyloplasts, and chromoplasts.Chelicerata: Late Ordovician (but see text) – RecentMT-RNR2: Mitochondrially encoded 16S RNA (often abbreviated as 16S) is a mitochondrial ribosomal RNA (rRNA) that in humans is encoded by the MT-RNR2 gene. The MT-RNR2 gene also encodes the Humanin polypeptide that has been the target of Alzheimer's disease research.ParaHox: The ParaHox gene cluster is an array of homeobox genes (involved in morphogenesis, the regulation of patterns of anatomical development) from the Gsx, Xlox (Pdx) and Cdx gene families.Alliance for Zero Extinction: Formed in 2000 and launched globally in 2005, the Alliance for Zero Extinction (AZE) comprises 100 non-governmental biodiversity conservation organizations working to prevent species extinctions by identifying and safeguarding sites where species evaluated to be Endangered or Critically Endangered under International Union for Conservation of Nature (IUCN) criteria only exist at one location on earth."Zero Extinction - Home.Gene duplication: Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene.Oxymonad: The Oxymonads are a group of flagellated protozoa found exclusively in the intestines of termites and other wood-eating insects. Along with the similar parabasalid flagellates, they harbor the symbiotic bacteria that are responsible for breaking down cellulose.List of sequenced eukaryotic genomesGlobal microbial identifier: The genomic epidemiological database for global identification of microorganisms or global microbial identifier (GMI) is a platform for storing whole genome sequencing (WGS) data of microorganisms, for the identification of relevant genes and for the comparison of genomes to detect and track-and-trace infectious disease outbreaks and emerging pathogens. The database holds two types of information: 1) genomic information of microorganisms, linked to, 2) metadata of those microorganism such as epidemiological details.Bird trapping: Bird trapping techniques to capture wild birds include a wide range of techniques that have their origins in the hunting of birds for food. While hunting for food does not require birds to be caught alive, some trapping techniques capture birds without harming them and are of use in ornithology research.Cambrian–Ordovician extinction eventProtein primary structure: The primary structure of a peptide or protein is the linear sequence of its amino acid structural units, and partly comprises its overall biomolecular structure. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end.PSI Protein Classifier: PSI Protein Classifier is a program generalizing the results of both successive and independent iterations of the PSI-BLAST program. PSI Protein Classifier determines belonging of the found by PSI-BLAST proteins to the known families.Symbiosis Center of Health Care: Symbiosis Center of Health Care (SCHC) is an organization under Symbiosis Society which takes care of health of symbiosis family be it student or staff.http://www.Ontario Genomics Institute: The Ontario Genomics Institute (OGI) is a not-for-profit organization that manages cutting-edge genomics research projects and platforms.The Ontario Genomics Institute OGI also helps scientists find paths to the marketplace for their discoveries and the products to which they lead, and it works through diverse outreach and educational activities to raise awareness and facilitate informed public dialogue about genomics and its social impacts.Lasiodiplodia: Lasiodiplodia is a genus of fungi in the family Botryosphaeriaceae. There are 21 species.Anthoceros: Anthoceros is a genus of hornworts in the family Anthocerotaceae. The genus is global in its distribution.Clonal Selection Algorithm: In artificial immune systems, Clonal selection algorithms are a class of algorithms inspired by the clonal selection theory of acquired immunity that explains how B and T lymphocytes improve their response to antigens over time called affinity maturation. These algorithms focus on the Darwinian attributes of the theory where selection is inspired by the affinity of antigen-antibody interactions, reproduction is inspired by cell division, and variation is inspired by somatic hypermutation.Domain (biology): In biological taxonomy, a domain (also superregnum, superkingdom, empire, or regio) is the highest taxonomic rank of organisms in the three-domain system of taxonomy designed by Carl Woese, an American microbiologist and biophysicist. According to the Woese system, introduced in 1990, the tree of life consists of three domains: Archaea (a term which Woese created), Bacteria, and Eukaryota.EcosystemExogenous bacteria: Exogenous bacteria are microorganisms introduced to closed biological systems from the external world. They exist in aquatic and terrestrial environments, as well as the atmosphere.Eukaryotic elongation factors: Eukaryotic elongation factors are very similar to those in prokaryotes.Microcotyle: Microcotyle is a genus which belongs to the phylum Platyhelminthes and class Monogenea. It is an ectoparasite that affects its host by attaching itself as a larva on the gills of the fish and grows into adult stage.Mac OS X Server 1.0AmbulocetidaeBaltic sculpin: The Baltic sculpinBaltic sculpin (Cottus microstomus) at EOL (Cottus microstomus) is a species of sculpin, a European freshwater fish in the Cottidae family. It is widespread in the Dniester drainage (Black Sea basin), Odra and Vistula drainages (southern Baltic basin), most likely extending further east to Gulf of Finland.Tokay gecko: The tokay gecko (Gekko gecko) is a nocturnal arboreal gecko, ranging from northeast India, Bhutan, Nepal, Bangladesh, throughout Southeast Asia, Philippines to Indonesia and western New Guinea. Its native habitat is rainforest trees and cliffs, and it also frequently adapts to rural human habitations, roaming walls and ceilings at night in search of insect prey.Cyanidioschyzon merolae: C. merolae is a small (2μm), club-shaped, unicellular haploid red alga adapted to high sulfur acidic hot spring environments (pH 1.Blepharisma japonicum: Blepharisma japonicum is a species of protozoans, that can be found either in water or soilHabitat of Japan.Caninia (genus)Intergenic region: An Intergenic region (IGR) is a stretch of DNA sequences located between genes. Intergenic regions are a subset of Noncoding DNA.Rakiura (genus): Rakiura is a genus of Trichoptera (caddisfly). The genus contains only one species, R.Nippleus Erectus: Nippleus Erectus was a drummer of GWAR (played by former White Cross member Rob Mosby), who did all the drumming for Hell-O. He is also credited for the drums on Scumdogs of the Universe, though it was Jizmak Da Gusha who played them.Marine fungi: Marine fungi are species of fungi that live in marine or estuarine environments. They are not a taxonomic group but share a common habitat.MoniliellaRespiratory system of gastropods: The respiratory system of gastropods varies greatly in form. These variations were once used as a basis for dividing the group into subclasses.Transport in Madagascar: == Railways ==Bodo people: (Assam)Haematococcus pluvialis: Haematococcus pluvialis is a freshwater species of Chlorophyta from the family Haematococcaceae. This species is well known for its high content of the strong antioxidant astaxanthin, which is important in aquaculture, and cosmetics.Thermal cyclerPlasmodium eylesi: Plasmodium eylesi is a parasite of the genus Plasmodium subgenus Plasmodium.Puccinia striiformis var. striiformis: Puccinia striiformis var. striiformis is a plant pathogen.Index of geology articles: This is a list of all articles related to geology that cannot be readily placed on the following subtopic pages:HEPN domain: In molecular biology, the HEPN domain (higher eukaryotes and prokaryotes nucleotide-binding domain) is a region of approximately 110 amino acids found in the C terminus of sacsin, a chaperonin implicated in an early-onset neurodegenerative disease in human, and in many bacterial and archaea proteins. There are three classes of proteins with HEPN domains:Extracellular: In cell biology, molecular biology and related fields, the word extracellular (or sometimes extracellular space) means "outside the cell". This space is usually taken to be outside the plasma membranes, and occupied by fluid.Confusion (New Order song): "Confusion" is a single released by British group New Order in August 1983 with the catalogue number FAC 93.New Order - Confusion at discogs.Alkalimonas: Alkalimonas is a genus in the phylum Proteobacteria (Bacteria).Erythronium japonicum: Katakuri (Erythronium japonicum; ) is a pink-flowered species trout lily, belonging to the Lily family and native to Japan, Korea, the Russian Far East (Sakhalin Island, Kuril Islands) and northeastern China (Jilin and Liaoning).Flora of China v 24 p 126Kew World Checklist of Selected Plant Families It is a spring ephemeral, blooming April–June in woodlands.Tithonia diversifoliaUtiaritichthys: Utiaritichthys is a genus of serrasalmid found in the Amazon and Orinoco basins in tropical South America.Nucleomorph: Nucleomorphs are small, vestigial eukaryotic nuclei found between the inner and outer pairs of membranes in certain plastids. They are thought to be vestiges of primitive red and green algal nuclei that engulfed a prokaryote (plastid).

(1/52004) A novel genetic screen for snRNP assembly factors in yeast identifies a conserved protein, Sad1p, also required for pre-mRNA splicing.

The assembly pathway of spliceosomal snRNPs in yeast is poorly understood. We devised a screen to identify mutations blocking the assembly of newly synthesized U4 snRNA into a functional snRNP. Fifteen mutant strains failing either to accumulate the newly synthesized U4 snRNA or to assemble a U4/U6 particle were identified and categorized into 13 complementation groups. Thirteen previously identified splicing-defective prp mutants were also assayed for U4 snRNP assembly defects. Mutations in the U4/U6 snRNP components Prp3p, Prp4p, and Prp24p led to disassembly of the U4/U6 snRNP particle and degradation of the U6 snRNA, while prp17-1 and prp19-1 strains accumulated free U4 and U6 snRNA. A detailed analysis of a newly identified mutant, the sad1-1 mutant, is presented. In addition to having the snRNP assembly defect, the sad1-1 mutant is severely impaired in splicing at the restrictive temperature: the RP29 pre-mRNA strongly accumulates and splicing-dependent production of beta-galactosidase from reporter constructs is abolished, while extracts prepared from sad1-1 strains fail to splice pre-mRNA substrates in vitro. The sad1-1 mutant is the only splicing-defective mutant analyzed whose mutation preferentially affects assembly of newly synthesized U4 snRNA into the U4/U6 particle. SAD1 encodes a novel protein of 52 kDa which is essential for cell viability. Sad1p localizes to the nucleus and is not stably associated with any of the U snRNAs. Sad1p contains a putative zinc finger and is phylogenetically highly conserved, with homologues identified in human, Caenorhabditis elegans, Arabidospis, and Drosophila.  (+info)

(2/52004) The nuclear receptor superfamily has undergone extensive proliferation and diversification in nematodes.

The nuclear receptor (NR) superfamily is the most abundant class of transcriptional regulators encoded in the Caenorhabditis elegans genome, with >200 predicted genes revealed by the screens and analysis of genomic sequence reported here. This is the largest number of NR genes yet described from a single species, although our analysis of available genomic sequence from the related nematode Caenorhabditis briggsae indicates that it also has a large number. Existing data demonstrate expression for 25% of the C. elegans NR sequences. Sequence conservation and statistical arguments suggest that the majority represent functional genes. An analysis of these genes based on the DNA-binding domain motif revealed that several NR classes conserved in both vertebrates and insects are also represented among the nematode genes, consistent with the existence of ancient NR classes shared among most, and perhaps all, metazoans. Most of the nematode NR sequences, however, are distinct from those currently known in other phyla, and reveal a previously unobserved diversity within the NR superfamily. In C. elegans, extensive proliferation and diversification of NR sequences have occurred on chromosome V, accounting for > 50% of the predicted NR genes.  (+info)

(3/52004) Isolation of zebrafish gdf7 and comparative genetic mapping of genes belonging to the growth/differentiation factor 5, 6, 7 subgroup of the TGF-beta superfamily.

The Growth/differentiation factor (Gdf) 5, 6, 7 genes form a closely related subgroup belonging to the TGF-beta superfamily. In zebrafish, there are three genes that belong to the Gdf5, 6, 7 subgroup that have been named radar, dynamo, and contact. The genes radar and dynamo both encode proteins most similar to mouse GDF6. The orthologous identity of these genes on the basis of amino acid similarities has not been clear. We have identified gdf7, a fourth zebrafish gene belonging to the Gdf5, 6, 7 subgroup. To assign correct orthologies and to investigate the evolutionary relationships of the human, mouse, and zebrafish Gdf5, 6, 7 subgroup, we have compared genetic map positions of the zebrafish and mammalian genes. We have mapped zebrafish gdf7 to linkage group (LG) 17, contact to LG9, GDF6 to human chromosome (Hsa) 8 and GDF7 to Hsa2p. The radar and dynamo genes have been localized previously to LG16 and LG19, respectively. A comparison of syntenies shared among human, mouse, and zebrafish genomes indicates that gdf7 is the ortholog of mammalian GDF7/Gdf7. LG16 shares syntenic relationships with mouse chromosome (Mmu) 4, including Gdf6. Portions of LG16 and LG19 appear to be duplicate chromosomes, thus suggesting that radar and dynamo are both orthologs of Gdf6. Finally, the mapping data is consistent with contact being the zebrafish ortholog of mammalian GDF5/Gdf5.  (+info)

(4/52004) Novel endotheliotropic herpesviruses fatal for Asian and African elephants.

A highly fatal hemorrhagic disease has been identified in 10 young Asian and African elephants at North American zoos. In the affected animals there was ultrastructural evidence for herpesvirus-like particles in endothelial cells of the heart, liver, and tongue. Consensus primer polymerase chain reaction combined with sequencing yielded molecular evidence that confirmed the presence of two novel but related herpesviruses associated with the disease, one in Asian elephants and another in African elephants. Otherwise healthy African elephants with external herpetic lesions yielded herpesvirus sequences identical to that found in Asian elephants with endothelial disease. This finding suggests that the Asian elephant deaths were caused by cross-species infection with a herpesvirus that is naturally latent in, but normally not lethal to, African elephants. A reciprocal relationship may exist for the African elephant disease.  (+info)

(5/52004) Evolutionary relationships of pathogenic clones of Vibrio cholerae by sequence analysis of four housekeeping genes.

Studies of the Vibrio cholerae population, using molecular typing techniques, have shown the existence of several pathogenic clones, mainly sixth-pandemic, seventh-pandemic, and U.S. Gulf Coast clones. However, the relationship of the pathogenic clones to environmental V. cholerae isolates remains unclear. A previous study to determine the phylogeny of V. cholerae by sequencing the asd (aspartate semialdehyde dehydrogenase) gene of V. cholerae showed that the sixth-pandemic, seventh-pandemic, and U.S. Gulf Coast clones had very different asd sequences which fell into separate lineages in the V. cholerae population. As gene trees drawn from a single gene may not reflect the true topology of the population, we sequenced the mdh (malate dehydrogenase) and hlyA (hemolysin A) genes from representatives of environmental and clinical isolates of V. cholerae and found that the mdh and hlyA sequences from the three pathogenic clones were identical, except for the previously reported 11-bp deletion in hlyA in the sixth-pandemic clone. Identical sequences were obtained, despite average nucleotide differences in the mdh and hlyA genes of 1.52 and 3.25%, respectively, among all the isolates, suggesting that the three pathogenic clones are closely related. To extend these observations, segments of the recA and dnaE genes were sequenced from a selection of the pathogenic isolates, where the sequences were either identical or substantially different between the clones. The results show that the three pathogenic clones are very closely related and that there has been a high level of recombination in their evolution.  (+info)

(6/52004) Three receptor genes for plasminogen related growth factors in the genome of the puffer fish Fugu rubripes.

Plasminogen related growth factors (PRGFs) and their receptors play major roles in embryogenesis, tissue regeneration and neoplasia. In order to investigate the complexity and evolution of the PRGF receptor family we have cloned and sequenced three receptors for PRGFs in the teleost fish Fugu rubripes, a model vertebrate with a compact genome. One of the receptor genes isolated encodes the orthologue of mammalian MET, whilst the other two may represent Fugu rubripes orthologues of RON and SEA. This is the first time three PRGF receptors have been identified in a single species.  (+info)

(7/52004) Cloning, molecular analysis and differential cell localisation of the p36 RACK analogue antigen from the parasite protozoon Crithidia fasciculata.

The family of the RACK molecules (receptors for activated C kinases) are present in all the species studied so far. In the genus Leishmania, these molecules also induce a strong immune reaction against the infection. We have cloned and characterised the gene that encodes the RACK analogue from the parasite trypanosomatid Crithidia fasciculata (CACK). The molecule seems to be encoded by two genes. The sequence analysis of the cloned open reading frame indicates the existence of a high degree of conservation not only with other members of the Trypanosomatidae but also with mammalians. The study of the protein kinase C phosphorylation sites shows the presence of three of them, shared with the mammalian species, additional to those present in the other protozoa suggesting a certain phylogenetic distance between the protozoon Crithidia fasciculata and the rest of the Trypanosomatidae. The CACK-encoded polypeptide shows an additional sequence of four amino acids at the carboxy-terminal end, which produces a different folding of the fragment with the presence of an alpha-helix instead of the beta-sheet usual in all the other species studied. A similar result is elicited at the amino-terminal end by the change of three amino acid residues. The immunolocalisation experiments show that the CACK displays a pattern with a distribution mainly at the plasma membrane, different from that of the related Leishmania species used as control, that displays a distribution close to the nucleus. Altogether, the data suggest that the existence of the structural differences found may have functional consequences.  (+info)

(8/52004) Rhodanobacter lindaniclasticus gen. nov., sp. nov., a lindane-degrading bacterium.

Lindane-degrading activity under aerobic conditions has been observed in two bacterial strains: UT26, phenotypically identified as Sphingomonas paucimobilis, and a new single unidentified isolate named RP5557T. The rrs (16S rDNA) sequences for both strains and the phenotypic characteristics for the unidentified isolate RP5557T were determined. RP5557T does not have high identity (less than 90% in all cases) with any sequence in the GenBank or RDP databases. A phylogenetic analysis based on rrs sequences indicated that RP5557T belongs to the gamma-Proteobacteria in a coherent phylum that includes the genera Xanthomonas and Xylella (100% bootstrap), whereas UT26 is clearly separate from the Xanthomonas cluster. Based on the phylogenetic analyses and on the phenotypic characteristics, a new genus, Rhodanobacter, containing a single species, Rhodanobacter lindaniclasticus, is proposed for strain RP5557T (= LMG 18385T), which becomes the type strain.  (+info)


If ontogeny recapitulates phylogeny does that mean strict vegans oppose abortion?


Excellent question; it makes sense to me. 

If human embryos repeat the evolution of their species, wouldn't abortion be the same thing as killing an animal?

Don't people who justify abortion often say that a human embryo is not really human yet?


Other than the popular HIV, what other Simian Virus is equally commonly in a different non-human species?


HIV obviously isn't exclusive; it beginning to seems as though it is a particular virus under a branch of other viruses, it is under a phylogeny of sorts.  Could someone explain this to me a little further?  Thanks
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The Swine flu is always developing and needs to be monitored on a daily basis. Here is a reference to the best article and update resource I have found.


Biology are u good PART2?


multiple chioce=)

1.The combining of genetic information from two individuals to produce offspring is called?
    a. inheritance    b. sexaul reproduction  c. development d. asexaul reproduction

2. Scientists estimate the number of species of organisms on the earth are?
      a. 4 million  b. 20 million  c.40 million d. 8billion

3. The study of the interactions of organisms with one another and with the enviorment is called?
     a. ecology  b. phylogeny  c. morphology  d. evolution

4. In multicellular organisms, tissues are organized into:
     a. cells b. systems  c. organs  d. structures

5.Deoxyribonucleic acid contians the chemical code for?
   a. sperm  b. energy  c. egg d. traits

6. Organisms that acquire energy by making there own food are called?
    a.autotrophic  b. heterotrophic  c.unicellar  d. multicellular

YOU SMART????
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1.b
2.d
3.a
4.c---only one I am unsure about
5.d
6.a


Difference between fruits and vegetables?


I know this question has been asked before, but I want clarifications.  People say that fruits have internal seeds and are fleshy, while vegetables don't have seeds and tend to be less sweet.  I want to know the phylogeny of fruits and vegetables.  Does the traditional fruit/vegetable classification system reflect evolutionary similarity?  It sounds like this system is completely arbitrary, so why don't we scrap it and make a new, better system?

In addition, please classify the following as either fruit or vegetable (or neither... if possible): squash, pumpkin, beans, peppers (including chili peppers), tomatoes, cucumbers and pickles, carrots, nuts, lentils, strawberries.  I know that some of these may be obvious, but you might be surprised about the discrepancy that exists.  Thanks!
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fruits are sweet and vegetables are more bitter

squash:fruit
pumpkin:fruit
beans:protein
peppers:fruit
tomatoes:fruit
cucumbers:fruit
pickles:fruit
carrots:vegetable
nuts:protein
lentils:protein
strawberries:fruit