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

TLDR

The growing availability of phylogenetic and trait data for co‑occurring species has created a need for software that integrates ecological and evolutionary analyses. Phylocom computes a wide array of phylogenetic community structure and trait similarity metrics, performs hypothesis testing with multiple null models, assesses phylogenetic signal and correlated trait evolution, and offers utilities for data manipulation, tree and trait generation, and workflow integration. The open‑source software is available at http://phylodiversity.net/phylocom/ (contact [e-mail]).

Abstract

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: [e-mail]