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TreesPhylogenyEvolution, MolecularDecision TreesSequence Analysis, DNAMolecular Sequence DataSequence AlignmentRNA, Ribosomal, 16SDNA, RibosomalBiological EvolutionAlgorithmsSoftwareModels, GeneticGenetic VariationLikelihood FunctionsBase SequenceSpecies SpecificityTea Tree OilAmino Acid SequenceCluster AnalysisTupaiidaeDNA, BacterialGene Transfer, HorizontalSequence Homology, Nucleic AcidDNA, Ribosomal SpacerGenes, rRNADNA, MitochondrialBase CompositionSequence HomologyClassificationBayes TheoremUser-Computer InterfaceDatabases, GeneticComputer SimulationComputational BiologyMultigene FamilyTropical ClimateSequence Analysis, ProteinSequence Homology, Amino AcidComputer GraphicsBacterial Typing TechniquesPinusDNA, ChloroplastGenomicsQuercusRNA, BacterialRNA, Ribosomal, 18SEukaryotaTupaiaPolymerase Chain ReactionEcosystemGeographyGenome, ViralBacteriaGenome, BacterialGenomeInternetDNA, PlantCytochromes bRNA, RibosomalModels, StatisticalPlantsWoodMammalsArchaeaFagusAngiospermsBiodiversityMarkov ChainsGenetic SpeciationEucalyptusGene DuplicationConserved SequencePlant LeavesFicusKoreaPrimatesFungiSoil MicrobiologyPlant StemsGenes, BacterialVertebratesDNA PrimersChinaProkaryotic CellsSequence AnalysisProgramming LanguagesBacterial ProteinsGenetics, PopulationPopulusForestryBeetlesProteobacteriaDNA Barcoding, TaxonomicBirdsGenes, PlantTenericutesGenotypeSyntenyAlphaproteobacteria
ReplicatesLineagesGeneticSequencesSpeciesMaximum LikelihoodProteinsAnalysisGenotypesReconstructionStrainsGeneraDiversityMitochondrialRelationshipsDistanceSubsequentFamilyAnalysesFastaAnalysis was performedGenomeIsolateCladesSpecies identificationPhylipMosquitoCONCLUSIONSGroupingsReliabilityMolecularGene familyBranchesStronglyAlignmentProteinBranch lengthsExtractResultsDataOccursBelongMaximumSuggestCreateTotalRecentIndependentFound
Replicates3
  • We computed 1000 replicates for bootstrap support. (springeropen.com)
  • Numbers at nodes are bootstrap values based on 1000 replicates. (springeropen.com)
  • Phylogenetic reconstruction was performed in IQ-TREE with maximum likelihood based on the substitution model TPM3+F+I+G4 with bootstrap values deduced from 1000 replicates. (bvsalud.org)
Lineages4
  • Here, we show that across 12 plant species in two phylogenetic lineages of the Brassicaceae, variation in realized herbivore communities reveals a phylogenetic signal in the uncertainty of attack on individual plants. (biorxiv.org)
  • Species that cannot be easily distinguished based on morphology, but which form distinct phylogenetic lineages based on molecular markers, are often referred to as cryptic species. (springer.com)
  • Many AstVs sequences obtained from a given bat species clustered in different phylogenetic lineages, while others seem to reflect some level of host-virus association, but also with AstVs previously reported from Malagasy bats. (biomedcentral.com)
  • Based on population data, phylogenetic inferences from Pyrus mitogenomes supported two distinct maternal lineages of Asian cultivated pears. (biomedcentral.com)
Genetic3
  • Genetic and phylogenetic analyses revealed that this Sanmenxia H5N1 virus was a novel reassortant, possessing a Clade 2.3.2.1c HA gene and a H9N2-derived PB2 gene. (nature.com)
  • 18S rRNA was the first genetic marker used for phylogenetic classification of nematodes 4 . (nature.com)
  • Recent phylogenetic analyses based on multiple genetic markers indicated that F. fomentarius possibly contained cryptic species (Pristas et al. (springer.com)
Sequences8
  • Phylogenetic studies showed that the HCoV-HKU1 nucleoprotein gene was relatively conserved compared to NCBI reference sequences, while the 1ab gene of HCoV-NL63 showed more variation. (hindawi.com)
  • The sequences used for the tree were derived from 3 separate mitochondrial control region sequences. (wikipedia.org)
  • We sequenced the complete mt genome of W. compar and conducted phylogenetic analyses using concatenated coding sequences of 12 protein-coding genes (PCGs) by maximum likelihood and Bayesian inference. (nature.com)
  • Recent molecular analyses of mt genome sequences have provided selectable hypotheses for the phylogenetic relationships of nematodes based on 18S rRNA. (nature.com)
  • We conducted a phylogenetic analysis of the section, including samples of all species, using sequences of the ITS and ETS regions of nuclear ribosomal DNA. (bioone.org)
  • The phylogenetic analyses of the E6 and E7 sequences indicated that they belonged to sub-lineage A1 and sub-lineage B1, whereas the selective pressure analyses showed that only the E7 mutation sites 4R, 34E, and 52F were positive selection. (biomedcentral.com)
  • Table 1 Fomes sequences included in the phylogenetic analysis with information on the species identification, the newly sequenced voucher, the GenBank Accession number, and available information on geographic provenance as well as on host plant and isolation source. (springer.com)
  • means of phylogenetic analysis of its genomic sequences. (cdc.gov)
Species1
  • Phylogenetic analyses using Bayesian methods recovered a monophyletic grouping of all Dendrobium species (D. nobile, D. huoshanense, D. officinale, D. pendulum, D. strongylanthum and D. chrysotoxum). (plos.org)
Maximum Likelihood3
  • Phylogenetic trees were constructed by Maximum-likelihood and the Kimura 2-parameters methods by Molecular Evolutionary Genetics Analysis version 6.0. (biomedcentral.com)
  • The selection pressures acting on the E6 / E7 genes were estimated by Phylogenetic Analyses by Maximum Likelihood version 4.8 software. (biomedcentral.com)
  • Phylogenetic tree generated by the Maximum Likelihood method of MEGA4. (springeropen.com)
Proteins3
Analysis6
  • Phylogenetic analysis also showed that W. compar and W. siamensis formed a sister group. (nature.com)
  • Further phylogenetic analysis suggested specific family members of CYPs that may participate in the late steps during celastrol biosynthesis. (techscience.com)
  • Phylogenetic analysis divided these NAC transcription factors into 11 groups (A-K). Three PgNACs (− 073, − 29, and − 151) were found to be membrane-associated transcription factors. (biomedcentral.com)
  • Phylogenetic analysis placed A. ceylanicum isolated from dogs in one group with A. ceylanicum human isolates. (biomedcentral.com)
  • This hypothesis was tested based on phylogenetic analysis of the rDNA ITS region, morphological characters of basidiomes and pure cultures, growth rates and optimum growth temperature experiments, mycelial confrontation tests, enzyme activity tests and volatile organic compound (VOC) production. (springer.com)
  • Molecular phylogenetic analysis, tests on growth characteristics, enzyme assays, and comparative analysis of volatile compounds, were carried out for this purpose. (springer.com)
Genotypes1
  • Phylogenetic analyses were performed to determine norovirus genotypes. (biomedcentral.com)
Reconstruction1
  • The molecular survey of HCV provides some clues about the epidemiological status of the infections in a local scale and the phylogenetic and demographic reconstruction analyses complement this study by inferring whether the infections of certain subtypes are in a steady state or expanding. (cdc.gov)
Strains2
  • Soe, K.M., Htwe, A.Z., Moe, K., Abiko, T. and Yamakawa, T. (2020) Phylogenetic Diversity and Evaluation the Effectiveness of Indigenous Bradyrhizobium Strains for Myanmar Black Gram ( Vigna mungo L. Hepper) Cultivars. (scirp.org)
  • Furthermore, all GII.4 strains were phylogenetic analyzed based on their capsid P2 subdomains. (biomedcentral.com)
Genera1
  • Phylogenetic tree showing the relationships between detected strain N1A3101 and other members of the genus Glutamicibacter and other related genera. (springeropen.com)
Diversity1
  • Candidatus Nanohaloarchaeota, an archaeal phylum within the DPANN superphylum, is characterized by limited metabolic capabilities and limited phylogenetic diversity and until recently has been considered to exclusively inhabit hypersaline environments due to an obligate association with Halobacteria . (biomedcentral.com)
Mitochondrial1
  • This study aimed to determine the complete mitochondrial (mt) genome of W. compar and reconstruct its phylogenetic relationship with other nematodes. (nature.com)
Relationships2
  • The uniparental inheritance and non-recombinant nature of cp genomes make them potentially useful tools for inferring evolutionary and ancient phylogenetic relationships. (plos.org)
  • This study characterizes the variations in gene content, genome size, rearrangement rate, and the impact of domestication in Rosaceae mitogenomes and provides insights into their structural variation patterns and phylogenetic relationships. (biomedcentral.com)
Distance1
  • doi:10.1371/journal.pone.0006400 A neighbour-joining phylogenetic distance tree was constructed in PAUP4 with 1000 bootstrap replications to determine the strength of groupings. (wikipedia.org)
Subsequent1
  • Fast dispersal of pinewood nematode (PWN), the causal agent for the destructive pine wilt disease and subsequent infection of pine trees, is characterized by the high vector competence of pine sawyer beetles ( Monochamus spp. (elifesciences.org)
Family1
  • Rhus chinensis belongs to the plant family Anacardiaceae and is a common deciduous tree that is endemic to the warm temperate zone of Asia. (frontiersin.org)
Analyses6
  • Recent phylogenetic analyses based on the complete chloroplast genome sequence suggested strong support for the position of Vitaceae as the earliest diverging lineage of rosids and placed it as a sister to the remaining rosids. (frontiersin.org)
  • R2R3-MYB is the most abundant MYB subclass and potato R2R3-MYB members together with their Arabidopsis homologs were divided into 35 well-supported subgroups as the result of phylogenetic analyses. (mdpi.com)
  • Analyses on gene structure and protein motif revealed that members from the same subgroup shared similar exon/intron and motif organization, further supporting the results of phylogenetic analyses. (mdpi.com)
  • Phylogenetic analyses showed that different H1N1 variants circulated in that farm. (biomedcentral.com)
  • To examine the molecular evolution of NCX genes and understand the role of duplicated genes in the evolution of the vertebrate NCX gene family, we carried out phylogenetic analyses of NCX genes and compared NCX gene structures from sequenced genomes and individual clones. (biomedcentral.com)
  • Based on the criterion of parsimony, phylogenetic analyses of 35 craniodental characters strongly support the recent common ancestry of the new form and Holochilus. (diazilla.com)
Fasta1
Analysis was performed2
Genome2
  • To report the complete genome and phylogenetic analysis of a human monkeypox case detected in Colombia. (bvsalud.org)
  • Reads were aligned against the MPXV reference genome using minimap2 v.2.24 and phylogenetic inference was performed using maximum likelihood estimation. (bvsalud.org)
Isolate1
  • Phylogenetic analysis confirmed that the isolate could be assigned as new species of the Streptomyces , coded as Streptomyces sp. (springeropen.com)
Clades2
  • A phylogenetic tree constructed based on 70 protein-coding genes of 33 angiosperms showed that both Saxifragales and Vitaceae diverged from the rosid clade and formed two clades with 100% bootstrap value. (frontiersin.org)
  • Over the past three decades, several morphological and molecular phylogenetic studies have been used to access the relationships among the major clades, resulting in angiosperms being classified into 59 orders and 413 families ( The angiosperm phylogeny group III [APG III], 2009 ). (frontiersin.org)
Species identification3
  • Because many of the primary malaria vectors belong to the Hyrcanus Group, accurate species identification and phylogenetic relationship evaluation in this group are essential for understanding malaria transmission and its relationship with the evolution of Plasmodium spp. (biomedcentral.com)
  • BLAST, phylogenetic and character based methods as these methods has been practiced to accurate species identification ( Sarkar et al. (animalscipublisher.com)
  • 2012). The present study is aimed to identify the two species of Puntius using the different computational methods e.g., distance, phylogenetic, (topology) similarity based and character attribute (CA) that used in the species identification as single methods may provide sometime false results ( van Velzen et al. (animalscipublisher.com)
Phylip2
  • You must make the tree yourself (on paper) using the results OR get the PHYLIP package and use the tree drawing facilities there. (bugaco.com)
  • Get the PHYLIP package anyway if you are interested in trees). (bugaco.com)
Mosquito1
  • Compared to cox 1, ITS2 is a more reliable tool for studying phylogenetic relationships among closely related mosquito taxa. (biomedcentral.com)
CONCLUSIONS2
  • CONCLUSIONS: Our results imply that despite having a broad range of mycorrhizal partners, T. japonicum was predominantly associated with a single fungal taxon at most of the sites among the host-tree species investigated. (datadryad.org)
  • Conclusions: Phylogenetic relationship analysis showed two genetically distinct Aedes aegypti in Saudi Arabia derived from dual African ancestor. (ijbiotech.com)
Groupings2
  • doi:10.1371/journal.pone.0006400 A neighbour-joining phylogenetic distance tree was constructed in PAUP4 with 1000 bootstrap replications to determine the strength of groupings. (wikipedia.org)
  • 5) BOOTSTRAPPING is a method for deriving confidence values for the groupings in a tree (first adapted for trees by Joe Felsenstein). (bugaco.com)
Reliability1
  • The reliability of the phylogenetic trees were assessed by bootstrap resampling (1000 datasets). (unibo.it)
Molecular2
  • certain on biological grounds) OR if you assume a degree of constancy in the 'molecular clock', you can place the root in the 'middle' of the tree (roughly equidistant from all tips). (bugaco.com)
  • An ultrametric tree is simply a global molecular clock and can be easily generate in PAML using a single evolutionary rate. (stackexchange.com)
Gene family1
  • I would like to see use the ultrametric tree for Ranger-DTL for infer gene family evolution by speciation, gene duplication, horizontal gene transfer, and gene loss. (stackexchange.com)
Branches1
  • To estimate the relative robustness of the branches, the bootstrap method was used with 1000 replicates. (datadryad.org)
Strongly1
  • This distinction in flowering plants has offered key challenges to evolutionary biologists investigating the origin and evolution of their traits, and determining these issues precisely depends on having a well agreed upon and strongly supported phylogenetic framework. (frontiersin.org)
Alignment2
  • -intree with -n will read a separate starting tree for each alignment. (ubuntu.com)
  • 1) Before calculating a tree, you must have an ALIGNMENT in memory. (bugaco.com)
Protein1
  • The homology modeling of protein domains and a phylogenetic analysis of ParDAM5 suggest its functional integrity. (frontiersin.org)
Branch lengths2
  • Any branch lengths in the starting trees are ignored. (ubuntu.com)
  • This gives an UNROOTED tree and all branch lengths. (bugaco.com)
Extract1
Results1
  • The results of phylogenetic tree analysis indicated that the partial S gene sequencing had nearly the same phylogenetic tree as that of the S gene sequencing (shown as Figure 1 , 2 , 3 ). (biomedcentral.com)
Data2
  • Data were resampled with 1000 bootstrap iterations. (xenbase.org)
  • Even if none of the distances in a data set exceed the reliable threshold, if you bootstrap the data, some of the bootstrap distances may randomly exceed the safe limit. (bugaco.com)
Occurs1
  • drawing N trees (1 from each sample) and counting how many times each grouping from the original tree occurs in the sample trees. (bugaco.com)
Belong1
Maximum2
  • The phylogenetic tree was constructed by MEGA6 using the maximum-likelihood method. (xenbase.org)
  • The phylogenetic tree was obtained using the maximum likelihood method based on the Kimura two-parameter model. (datadryad.org)
Suggest1
  • Therefore, Please suggest me how to generate ultrametric tree from the rooted species tree. (stackexchange.com)
Create1
Total4
  • A total of 117 MATE transporters were identified in soybean and their potential functions were proposed by phylogenetic analysis with known plant MATE transporters. (biomedcentral.com)
  • In total, 144 individuals were collected from 28 host tree species at 20 sites across 1300 km. (datadryad.org)
  • A total of 1000 swabs were collected from poultry from 7 Lebanese governorates between March and June 2017. (who.int)
  • el cual se purificó el ADN total de la muestra mediante un método basado en columnas, Katherine Laiton-Donato, Diego A. Álvarez-Díaz, seguido de la secuenciación directa en la plataforma Nanopore GridION. (bvsalud.org)
Recent1
  • Recent phylogenetic studies suggested that it should be placed in various alternative families including Caryophyllaceae, asteraceae, Saxifragaceae, Dilleniaceae, or with the rest of the rosid families. (frontiersin.org)
Independent2
  • Each of these species was represented as an independent lineage in the phylogenetic tree. (biomedcentral.com)
  • The phylogenetic analysis indicates an independent evolution of BpHyal when compared to other hyaluronidases. (biomedcentral.com)
Found2
  • You can alternatively generate it de novo via UPGMA neighbor-joining tree which is found in the MEGAX package (which is probably easier and considered a technical definition of an ultrametric tree). (stackexchange.com)
  • The] island we found uninhabited, and it contained This extinct rodent is diagnosed and deplenty of trees, and so many birds, both marine and scribed as a new genus and species. (diazilla.com)