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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 citations

 (143)
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Areas of high conservation value at risk by plant invaders in Georgia under climate change

2018
Ecol Evol
PMCID: 5938453
PMID: 29760885
DOI: 10.1002/ece3.4005
call_split See protocol

[…] cally 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) of the select […]

library_books

Disentangling the role of floral sensory stimuli in pollination networks

2018
Nat Commun
PMCID: 5847531
PMID: 29531220
DOI: 10.1038/s41467-018-03448-w

[…] 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 time […]

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Geographic range velocity and its association with phylogeny and life history traits in North American woody plants

2018
Ecol Evol
PMCID: 5838057
PMID: 29531682
DOI: 10.1002/ece3.3880
call_split See protocol

[…] 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 pairs […]

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Phylogeny and source climate impact seed dormancy and germination of restoration relevant forb species

2018
PLoS One
PMCID: 5798788
PMID: 29401470
DOI: 10.1371/journal.pone.0191931
call_split See protocol

[…] ance 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 ma […]

library_books

Functional and phylogenetic diversity determine woody productivity in a temperate forest

2018
Ecol Evol
PMCID: 5838064
PMID: 29531662
DOI: 10.1002/ece3.3857

[…] ylogenetic 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 of the angi […]

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Functional trade‐offs and the phylogenetic dispersion of seed traits in a biodiversity hotspot of the Mountains of Southwest China

2018
Ecol Evol
PMCID: 5817125
PMID: 29468038
DOI: 10.1002/ece3.3805
call_split See protocol

[…] We built phylogenetic trees, resolved to the genus level, using the “TPL” function in “plantlist” package (Zhang, ) of R3.2.4 for Windows (R Core Team, ) and the supertree of Phylomatic (http://phylodiversity.net) based on the Angiosperm Phylogeny Group III. Branch lengths were assigned using the Bladj function of the Phylocom software, which assigned nodal ages down to th […]

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

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