Mitochondrial DNA
Data from the comparisons is used to construct a network of relationships among the sequences, which provides an estimate of ... Molecular and cellular biology portal Molecular Anthropology portal Evolutionary biology portal. ... Although most of them focus on sequence data, some of them include phylogenetic or functional information. MitoSatPlant: ... Moreover, there is data supporting the involvement of helix-distorting intrinsically curved regions and long G-tetrads in ...
List of phylogenetic tree visualization software
... phylogenetic inference and data visualization for sequence based typing methods". BMC Bioinformatics. 13: 7. doi:10.1186/1471- ... Molecular Biology and Evolution. 33 (8): 2163-6. doi:10.1093/molbev/msw080. PMC 4948708 . PMID 27189561. Retrieved 21 April ... a software environment for sequence data". Nucleic Acids Res. 32 (4): 1363-71. doi:10.1093/nar/gkh293. PMC 390282 . PMID ... a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization". Bioinformatics. doi: ...
Ancestral reconstruction
Rather than inferring the ancestral DNA sequence, one may be interested in the larger-scale molecular structure and content of ... The majority of these software packages are designed for analyzing genetic sequence data. For example, PAML is a collection of ... These states include the genetic sequence (ancestral sequence reconstruction), the amino acid sequence of a protein, the ... HyPhy, Mesquite, and MEGA are also software packages for the phylogenetic analysis of sequence data, but are designed to be ...
Phylogenesis
Phylogenetics is the branch of life science concerned with the analysis of molecular sequencing data to study evolutionary ... These terms may be confused with the term phylogenetics, the application of molecular - analytical methods (i.e. molecular ... genetic sequencing data and computational phylogenetics are now commonly used and the parsimony criterion has been abandoned by ... such as DNA sequences or overall morpho-anatomical, ethological, and other characteristics. The result of these analyses is a ...
Molecular phylogenetics
... is one aspect of molecular systematics, a broader term that also includes the use of molecular data in ... Typical molecular systematic analyses require the sequencing of around 1000 base pairs. At any location within such a sequence ... provides a molecular clock for dating divergence. Molecular phylogeny uses such data to build a "relationship tree" that shows ... ISBN 0-41202-231-1. Soltis, P.S., Soltis, D.E., and Doyle, J.J. (1998) Molecular Systematics of Plants II: DNA Sequencing. ...
Protein primary structure
Peptides can be directly sequenced, or inferred from DNA sequences. Large sequence databases now exist that collate known ... Despite these data and later evidence that proteolytically digested proteins yielded only oligopeptides, the idea that proteins ... CS1 maint: Multiple names: authors list (link) Hausman, Robert E.; Cooper, Geoffrey M. (2004). The cell: a molecular approach. ... Sequence families are often determined by sequence clustering, and structural genomics projects aim to produce a set of ...
Structural alignment software
Sippl, M.; Wiederstein, M. (2012). "Detection of spatial correlations in protein structures and molecular complexes". Structure ... Sequence-based alignment Pair -- Pairwise Alignment (2 structures *only*); Multi -- Multiple Structure Alignment (MStA); C-Map ... a web application for highly accurate screening of spatial resiudue patterns in protein structure data". Bioinformatics. 32: ... Algorithms for Molecular Biology. 7 (4): 4. doi:10.1186/1748-7188-7-4. PMC 3298807 . PMID 22336468. Minami, S.; Sawada K.; ...
DNA nanoball sequencing
"State of the art de novo assembly of human genomes from massively parallel sequencing data". Human genomics. 4 (4): 271-7. doi: ... The high-molecular-weight DNA, often several megabase pairs long, is sonicated to break the DNA double-strands at random ... DNA nanoball sequencing is a high throughput sequencing technology that is used to determine the entire genomic sequence of an ... used DNA nanoball sequencing to sequence the genomes of a family of four relatives and were able to identify SNPs that may be ...
Mormopterus
Molecular sequencing data indicates that Mormopterus is paraphyletic. The closest relatives of M. kalinowski are members of ... "Toward a Molecular Phylogeny for the Molossidae (Chiroptera) of the Afro-Malagasy Region". Acta Chiropterologica. 13 (1): 1-16 ...
Near passerine
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... However, molecular data does not support the traditional arrangement; it is now clear that "near passerines" and "higher ... Johansson, Ulf S. & Ericson, Per G. P. (2003): Molecular support for a sister group relationship between Pici and Galbulae ( ...
Hamerkop
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ...
New World vulture
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-7. doi:10.1098/rsbl.2006.0523. PMC 1834003 . ... This was criticized, and an early DNA sequence study was based on erroneous data and subsequently retracted. There was then an ... They were especially common in the gut with Clostridia DNA sequence counts between 26% and 85% relative to total sequence ... Retrieved 3 August 2010 Avise, J. C.; Nelson, W. S. & Sibley, C. G. (1994) "DNA sequence support for a close phylogenetic ...
Turkey vulture
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 1-5. doi:10.1098/rsbl.2006.0523. PMC 1834003 . ... Media related to Turkey vulture at Wikimedia Commons Data related to Cathartes aura at Wikispecies Turkey vultures on eNature. ... 1991). Phylogeny and Classification of Birds: A Study in Molecular Evolution. Yale University Press. ISBN 0-300-04085-7. ... Molecular Phylogenetics and Evolution. 37 (2): 327-346. doi:10.1016/j.ympev.2005.04.010. ISSN 1055-7903. PMID 15925523. ...
Columbaves
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature (2015). doi:10.1038/nature15697 ...
Jacamar
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... "Molecular support for a sister group relationship between Pici and Galbulae (Piciformes sensu Wetmore 1960" (PDF). Journal of ...
Aequorlitornithes
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... 22 October 2015). "A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing". Nature. 526 (7574 ...
Galbuli
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... Johansson, Ulf S.; Ericson, Per G.P. (2003). "Molecular support for a sister group relationship between Pici and Galbulae ( ... Witt, C.C. (2004), Rates of Molecular Evolution and their Application to Neotropical Avian Biogeography, Ph.D. dissertation, ...
Puffbird
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... Molecular investigation of the Bucconidae in 2004 indicated that the nunlets (genus Nonnula) diverged from the common ancestor ... Johansson, Ulf S. & Ericson, Per G.P. (2003). "Molecular support for a sister group relationship between Pici and Galbulae ( ... Witt, C.C. (2004), Rates of Molecular Evolution and their Application to Neotropical Avian Biogeography, Ph.D. dissertation, ...
Pici (taxon)
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... Johansson, Ulf S. & Ericson, Per G.P. (2003). "Molecular support for a sister group relationship between Pici and Galbulae ( ...
Otidimorphae
... integration of molecular sequence data and fossils". Biology Letters. rsbl.royalsocietypublishing.org. 2 (4): 543-547. doi: ...
Mirandornithes
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... Molecular Phylogenetics and Evolution. 30 (1): 140-151. doi:10.1016/S1055-7903(03)00159-3. PMID 15022765. Mayr, G. (February ...
Tadarida
Molecular sequence data indicates Tadarida is not a monophyletic taxon. The closest relative of Tadarida aegyptiaca of Africa ... "Toward a Molecular Phylogeny for the Molossidae (Chiroptera) of the Afro-Malagasy Region". Acta Chiropterologica. 13 (1): 1-16 ...
Pelecaniformes
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... but molecular and morphological studies indicate they are not such close relatives. They have been placed in their own orders, ...
Cretaceous-Paleogene extinction event
December 2006). "Diversification of Neoaves: integration of molecular sequence data and fossils". Biol. Lett. 2 (4): 543-7. doi ... Based on molecular sequencing and fossil dating, Neoaves appeared to radiate after the K-Pg boundary. They even produced giant ... At present the most informative sequence of dinosaur-bearing rocks in the world from the K-Pg boundary is found in western ... In North America, the data suggests massive devastation and mass extinction of plants at the K-Pg boundary sections, although ...
Psittacopasserae
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... The group was proposed following an alignment of nuclear intron sequences by Shannon Hackett et al. in 2008, it was formally ... However, the technique requires very extensive genomic data - in the 2011 paper, approximately 200,000 retroposon-containing ...
Phyllanthaceae
"Molecular phylogenetic analysis of Euphorbiaceae sensu stricto based on plastid and nuclear DNA sequences and ovule and seed ... "Delimitation of Sauropus (Phyllanthaceae) Based on Plastid matK and Nuclear Ribosomal ITS DNA Sequence Data." Annals of Botany ... "Molecular phylogenetics of Phyllanthaceae: evidence from plastid matK and nuclear PHYC sequences". American Journal of Botany. ... based on nrITS and plastid matK DNA sequence data". American Journal of Botany. 93 (4): 637-655. doi:10.3732/ajb.93.4.637. PMID ...
Lesser yellow-headed vulture
... integration of molecular sequence data and fossils" (PDF). Biology Letters. 2 (4): 543-7. doi:10.1098/rsbl.2006.0523. PMC ... ISBN 0-19-854012-4. Sibley, Charles G.; Jon E. Ahlquist (1991). Phylogeny and Classification of Birds: A Study in Molecular ... Phylogeny and Classification of Birds: A Study in Molecular Evolution. Yale University Press. ISBN 0-300-04085-7. Accessed 2007 ...