Phylocom protocols

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Phylocom specifications


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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  • person_outline Campbell O. Webb <>

Publication for Phylocom

Phylocom in pipelines

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

[…] within family phylogenetic classification by adding the results obtained from the rbcl phylogeny. branch lengths and dated nodes for this megatree were obtained by applying the bladj algorithm of phylocom , with calibration ages from ., in order to standardize plot comparisons all diversity analyses described below were based on a fixed number (based on the plot with the fewest stems) […]

PMCID: 2939578
PMID: 20807394
DOI: 10.1186/1471-2148-10-263

[…] co-ortholog list, resulting in 339 groups of ubiquitous orthologs., to control for phylogenetic non-independence, we calculated independent contrast using the aot module implemented in the software phylocom []. in total, 109 species with ogt ranging from 15-100°c were included (additional file : supplemental table s4). the phylogenetic tree for these 109 species was obtained from the tree […]

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

[…] with maximum parsimony using the phylip 3.47 software package (dnapars program) with default settings., branch lengths for the backbone tree were calculated with the bladj program included with phylocom 3.41 . this program assigns ages to nodes that were estimated in reference , and then estimates the ages of remaining nodes so that they spread evenly between the dated nodes. this method […]

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Phylocom in publications

PMCID: 5938453
PMID: 29760885
DOI: 10.1002/ece3.4005

[…] 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., […]

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

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

PMCID: 5809509
PMID: 29434300
DOI: 10.1038/s41598-018-21266-4

[…] 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 […]

PMCID: 5828595
PMID: 29432167
DOI: 10.1073/pnas.1714977115

[…] 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., phylogenetic distance between all pairs of locations was calculated using the options comdist and comdistnt […]

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

[…] 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 […]

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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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