PHYLOCOM

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PHYLOCOM
Author(s) Campbell Webb, David Ackerly and Steven Kembel.
Category Population genetics, community phylogenetics, evolutionary ecology.
Licence Modified BSD license
Open source? Yes.
Last release version 4.2 – August 6, 2011.
Website http://www.phylodiversity.net/phylocom/


Contents

Program highlights and capabilities

“PHYLOCOM is a command-line application for manipulating ecological and phylogenetic data, calculating various metrics of phylogenetic and phenotypic community structure, and measuring trait conservatism and trait correlations” (Webb et al., 2011a).


“Phylomatic can be used to rapidly develop a phylogeny for any plant community. This phylogeny can then be input into the PHYLOCOM program to measure phylogenetic relatedness among species occurring together in samples, test hypotheses of community structure, or quantify patterns of trait evolution. If estimates exist for the ages of any node, these can be incorporated, as can branch lengths from other sources” (Webb et al., 2011a).


Phylcom can do the following (Webb et al., 2011):


Program requirements

Windows, Mac OS X, Linux/Unix.


Source publications

Authors recommend citing their program as follows (Webb et al., 2011):


Webb, C.O.; D.D. Ackerly & S.W. Kembel. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 24(18): 2098-2100.


Notes

  1. “This software is Free and Open Source, distributed under a BSD (‘3-clause’) license” (Webb et al., 2011a).
  2. “This software is provided by the copyright holders and contributors “as is” and any express or implied warranties, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose are disclaimed” (Webb et al., 2011a).


References


Additional information

Strauss, S.Y. & J.H. Burns. 2009. Community Phylogenetics [Online]. Website last modified on March 5, 2009 (accessed on November 28, 2011). Available at http://bodegaphylo.wikispot.org/Community_Phylogenetics


(For additional comments see discussion board Discussion).

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