Phylocom

Phylocom is a command-line application for manipulating ecological and phylogenetic data, calculating various metrics of phylogenetic and phenotypic community structure, and measuring trait conservatism and trait correlations.

The manual is in the doc/ directory.

Note that the C version of phylomatic bundled with phylocom is many years old. It it fast, and still works, but chokes on very large trees. Please consider using the latest version instead (see: {1}, {2}).

Citations

• 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. (PDF)
• Webb, C. O. & Donoghue, M. J. (2005) Phylomatic: tree assembly for applied phylogenetics. Molecular Ecology Notes 5: 181-183. (PDF)