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Protocols

Phylocom specifications

Information


Unique identifier OMICS_12479
Name Phylocom
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 4.2
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Campbell O. Webb

Publication for Phylocom

Phylocom citations

 (147)
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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

[…] 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 selected 114 endemic plants with the “picante” package (Blomberg, Garland & Ives, ; Kembel et al., ) in […]

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 between clades, using the most recently updated node ages. The phylogram o […]

call_split

Social status and parasitism in male and female vertebrates: a meta analysis

2018
Sci Rep
PMCID: 5827031
PMID: 29483573
DOI: 10.1038/s41598-018-21994-7
call_split See protocol

[…] ed divergence times from additional primary literature (Table ). We built ultrametric trees using the R package ape (version 3.4,) and adjusted node ages for published divergence times using BLADJ in Phylocom 4.2. […]

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Partitioning the regional and local drivers of phylogenetic and functional diversity along temperate elevational gradients on an East Asian peninsula

2018
Sci Rep
PMCID: 5809509
PMID: 29434300
DOI: 10.1038/s41598-018-21266-4
call_split See protocol

[…] l band. Finally, the γ component was quantified in each elevational band of each transect. The COMSTRUCT function for the α and γ components and the COMDIST function for the β components were used in Phylocom 4.2. We used the phylogenetic trees and trait dendrograms described in “Phylogenetic tree and functional trait dendrogram” to calculate the components of both dispersions.One of the main aims […]

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Phylogenetic classification of the world’s tropical forests

2018
Proc Natl Acad Sci U S A
PMCID: 5828595
PMID: 29432167
DOI: 10.1073/pnas.1714977115
call_split See protocol

[…] disjunct species occurrences in the phylogeny of Zanne et al. () were placed at the most basal node connecting the disjunct species. This phylogeny was subsequently dated using the BLADJ function in Phylocom v4.2 (), using taxon ages given in Magallón et al. () for the age file. […]

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

[…] ch lengths were estimated for this “super‐tree” based on the time of the angiosperm‐wide divergence. Undated nodes were interpolated using the algorithm of the branch length adjustment (BLADJ) in the Phylocom software (Webb, Ackerly, & Kembel, ). The PD was calculated as the sum of the branch lengths for the species present in a particular quadrat. As a consequence, the PD was influenced not only […]

Citations

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Phylocom institution(s)
Arnold Arboretum, Harvard University, Cambridge, MA, USA; Department of Integrative Biology, University of California, Berkeley, CA, USA
Phylocom funding source(s)
Phylocom development has been supported by grants 0212873 and 0515520 from the US NSF, by NSERC, by The Arnold Arboretum of Harvard University, and the Yale Institute of Biospheric Studies.

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