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Phylomatic specifications

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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

 (103)
library_books

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

2018
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) […]

library_books

Disentangling the role of floral sensory stimuli in pollination networks

2018
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 […]

library_books

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

2018
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 […]

library_books

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

2018
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 […]

library_books

Functional and phylogenetic diversity determine woody productivity in a temperate forest

2018
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 […]

library_books

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

2018
PMCID: 5817125
PMID: 29468038
DOI: 10.1002/ece3.3805

[…] of each photograph., 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 […]


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

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