Phylocom

Software for the Analysis of Phylogenetic Community Structure and Character Evolution, with Phylomatic

Features

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). Now 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 much 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. NEW: detects UNIX/Windows/Mac line-endings in your input files.

Obtaining and running Phylocom

The Phylocom distribution consists of C source code, Mac OS X and Windows binaries, manual, and example files. Read the manual for assistance installing and running the software.

DOWNLOAD at Github

(Chinese version of the manual is available, translated by Jinlong Zhang)

Development

We are now using github for development and distribution, and welcome pull requests.

Support

If you think you have found a bug, or are requesting new features, please open an issue on Github.

Other resources

Sharon Strauss and Jean Burns: phylocom tutorial.
Steve Vamosi further modified the above: phylocom tutorial.
The picante R package provides several functions for reading and writing phylocom-formatted data.
The phylocomr R package from ROpenSci.

Citing Phylocom

If you use results derived from Phylocom analyses in your publications, please cite:

Webb, C. O., Ackerly, D. D. & Kembel, S. W. (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics, 24: 2098-2100. DOI:10.1093/bioinformatics/btn358.

License

Phylocom is now released under a Modified (aka Simplified or 3-clause) BSD License (as of version 4.0 beta). See also the OSI, and Creative Commons listings.

Acknowledgments

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. See the manual for full acknowledgments.