Phylocom

Phylocom

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

Current version: 4.2

© 2024 Campbell Webb,
David
Ackerly, Steven
Kembel

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.

DOWNLOAD
PHYLOCOM & MANUAL

(Also, a Chinese
version of the manual, 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.

For assistance running the software, please subscribe and
post to this mailing list: phylocom-user.
Please read the manual first!

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.

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]

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 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.