Phylomatic protocols

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Phylomatic specifications

Information


Unique identifier OMICS_08886
Name Phylomatic
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Campbell O. Webb <>

Information


Unique identifier OMICS_08886
Name Phylomatic
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 3.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Campbell O. Webb <>

Publication for Phylomatic

Phylomatic in pipelines

 (4)
2017
PMCID: 5574787
PMID: 28861250
DOI: 10.1002/ece3.3226

[…] ronquist, ). to guide the search, we created a topological constraint tree from a published super tree (r20100428; angiosperm phylogeny group, ), pruned to the taxa used in our experiment using phylomatic (webb & donoghue, ). two independent markov chains were run, each with four heated chains for 5 million generations. the final average standard deviation of split frequencies […]

2017
PMCID: 5733559
PMID: 29321791
DOI: 10.3389/fpls.2017.02134

[…] each family, the positions of species were resolved with the barcode sequence data. according to this method, a phylogenetic tree was first generated for the sampled species using the online program phylomatic (webb and donoghue, ). this tree specified the taxonomic relationship of the 32 families, but within each family species were arrayed as a polytomy. the topology of this tree was defined […]

2013
PMCID: 3729948
PMID: 23936268
DOI: 10.1371/journal.pone.0071464

[…] had a bootstrap node support >80. below the family level, most of the genera appeared well resolved although with lower bootstrap support values. we then used the apgiii phylogeny as generated by phylomatic as our family level backbone phylogeny and resolved the within family phylogenetic classification by adding the results obtained from the rbcl phylogeny. branch lengths and dated nodes […]

2009
PMCID: 2740862
PMID: 19763265
DOI: 10.1371/journal.pone.0007071

[…] files., i created a phylogeny for all the herbaceous old field plants i surveyed by combining a backbone tree based on the apg phylogeny (http://www.mobot.org/mobot/research/apweb/) generated by phylomatic (http://www.phylodiversity.net/phylomatic/phylomatic.html) with subtrees created using downloaded sequences. i made three such trees for three families that lacked resolution […]


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Phylomatic in publications

 (101)
PMCID: 5938453
PMID: 29760885
DOI: 10.1002/ece3.4005

[…] nonbiased sample of all the endemics. to do so, we constructed the phylogenetic tree of all georgian endemics (n = 279) and the selected georeferenced endemics (n = 114) with the online program phylomatic (webb & donoghue, ) and calculated the branch lengths for both trees with the program phylocom version 4.2 (webb et al., ). we then calculated the mean pairwise distance (mpd) […]

PMCID: 5847531
PMID: 29531220
DOI: 10.1038/s41467-018-03448-w

[…] in the community (supplementary table ). therefore, for this species, apparency could not be calculated in relation to the co-flowering plants., plant phylogeny was built with the online software phylomatic v.3 (tree r20120829). we used ‘bladj’ algorithm in the software phylocom v.4.2 (ref. ) in order to adjust branch lengths of the phylogeny so as to correspond to evolutionary divergence […]

PMCID: 5838057
PMID: 29531682
DOI: 10.1002/ece3.3880

[…] quaternary velocity estimates was derived from the apg iii seed plant phylogeny reference tree (version 12; angiosperm phylogeny group, ) that is contained within the tree building software package, phylomatic (http://phylodiversity.net/phylomatic; webb, ackerly, & kembel, ). the apg supertree has been widely used in plant comparative phylogenetic analyses (e.g., lustenhouwer et al., ). two […]

PMCID: 5798788
PMID: 29401470
DOI: 10.1371/journal.pone.0191931

[…] matrices of germination traits, phylogenetic branch distances, and climatic data. to produce a distance matrix for phylogenetic relationships among species, a phylogenetic tree was created using phylomatic version 3 using the stored tree from zanne et al. 2014 [,]. the branch lengths of the tree, in millions of years, were used to create a distance matrix with cophenetic distances., distance […]

PMCID: 5838064
PMID: 29531662
DOI: 10.1002/ece3.3857

[…] diversity index (pd), which is based on the species’ evolutionary distances. a phylogenetic tree which includes 32 species in the study area was constructed using an informatics tool named phylomatic. phylomatic utilizes the phylogeny of angiosperm phylogeny group iii as a backbone (webb & donoghue, ). the branch lengths were estimated for this “super‐tree” based on the time […]


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Phylomatic institution(s)
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA

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