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Bioinformatics Advance Access originally published online on August 4, 2008
Bioinformatics 2008 24(18):2098-2100; doi:10.1093/bioinformatics/btn358
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Phylocom: software for the analysis of phylogenetic community structure and trait evolution

Campbell O. Webb 1,*, David D. Ackerly 2 and Steven W. Kembel 2

1Arnold Arboretum, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138 and 2Department of Integrative Biology, University of California, Berkeley, CA 94720, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: The increasing availability of phylogenetic and trait data for communities of co-occurring species has created a need for software that integrates ecological and evolutionary analyses.

Capabilities: Phylocom calculates numerous metrics of phylogenetic community structure and trait similarity within communities. Hypothesis testing is implemented using several null models. Within the same framework, it measures phylogenetic signal and correlated evolution for species traits. A range of utility functions allow community and phylogenetic data manipulation, tree and trait generation, and integration into scientific workflows.

Availability: Open source at: http://phylodiversity.net/phylocom/

Contact: cwebb{at}oeb.harvard.edu

Associate Editor: Martin Bishop

Received on May 16, 2008; revised on July 12, 2008; accepted on July 12, 2008

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