Phylocom
Features (Current version: 4.2)
- 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.
(Difference from version 4.1 to 4.2: minor bug fixes, and new options: new2fy and nodesigl)
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.
(Also, a Chinese version of the manual, translated by Jinlong Zhang)
You can also download version 3.41 of phylocom (released 2007-05-25).
Support
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!
Phylocom/phylomatic/ecovolve users mailing list: While the authors of phylocom endeavor to reply to your emails, sometimes things just get too much! Feel free to subscribe to our new mailing list: phylocom-user. You can use this list to request help from other users, offer tips and request new features. In order to reduce spam, the list archives are only available to registered members.
Other resources: Sharon Strauss and Jean Burns provide an excellent phylocom tutorial. The picante R package provides several functions for reading and writing phylocom-formatted data.
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. [LINK]
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.
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.