From The Molecular Ecology Resources bioinformatics wiki
|Author(s)||Campbell Webb, David Ackerly and Steven Kembel.|
|Category||Population genetics, community phylogenetics, evolutionary ecology.|
|Licence||Modified BSD license|
|Last release||version 4.2 – August 6, 2011.|
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):
- Calculate phylogenetic community structure metrics (Webb's NRI, NTI, Faith's PD, Rao's entropy) and compare observed patterns to those expected under various null models of community assembly and phylogeny structure (comstruct). Now, many metrics incorporate variation in taxon abundance.
- Calculate inter-sample phylogenetic distance for phylogenetic ordination and classification (comdist and comdistnt). [...] Incorporates null model testing of observed patterns.
- Comparative methods for the analysis of character evolution (aot; conservatism metrics, independent contrasts, lineages through time).
- Calculate trait distribution metrics within sample communities and compare to metrics for random community assembly (comtrait).
- Simulate phylogeny and trait evolution under various evolutionary models (ecovolve).
- Manipulate phylogenetic trees and ecological community data: convert Newick to Nexus format, prune and merge phylogenetic trees, add branch lengths to your supertrees, community data randomization using one of several null models, and [...] more.
- Turn species lists into phylogenies (with or without branch lengths) using the included standalone version of phylomatic and phylocom's bladj function.
- Handles large data sets (tested with >10,000 samples/taxa), polytomies, continuous and categorical characters. [...] Detects UNIX/Windows/Mac line-endings in your input files.
Windows, Mac OS X, Linux/Unix.
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.
- “This software is Free and Open Source, distributed under a BSD (‘3-clause’) license” (Webb et al., 2011a).
- “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).
- Webb, C.; D. Ackerly & S. Kembel. 2011. PHYLOCOM: Software for the Analysis of Phylogenetic Community Structure and Character Evolution, with Phylomatic [Online]. Website last modified in August 2011 (accessed on November 28, 2011). Available at http://www.phylodiversity.net/phylocom/
- Webb, C.; D. Ackerly & S. Kembel. 2011a. PHYLOCOM: Software for the analysis of phylogenetic community structure and character evolution (with Phylomatic and Ecovolve) - User’s Manual, version 4.2. Available with the program at http://www.phylodiversity.net/phylocom/
- 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).