Phylocom
Features (Current version: 4.0 beta)
- 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).
- 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/Widows/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.
You can also download version 3.41 of phylocom (released 2007-05-25).
If you think you have found a bug, have comments, or are having trouble, please contact Cam (general issues, phylomatic, ecovolve), Steve (comstruct- and comtrait-related), or David (aot-related). Please read the manual first!
Citing Phylocom
If you use results derived from Phylocom analyses in your publications, please cite:
- Webb, C.O., Ackerly, D.D., and Kembel, S.W. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Version 4.0. URL: http://www.phylodiversity.net/phylocom/.
Who is using Phylocom?
Studies we're aware of that have used Phylocom are being compiled on a CiteULike group. Please feel free to add any we've missed.
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.