Phylogemetric: A Python library for calculating phylogenetic network metrics

Summary

Phylogemetric is a Python library for calculating the δ-score (Holland et al. 2002) and Q-Residual (Gray, Bryant, and Greenhill 2010) for phylogenetic data. These methods are used in studies of linguistic and cultural evolution to quantify reticulation in data.

This Python library provides a command-line script interface for use on Nexus-formatted data (D. R. Maddison, Swofford, and Maddison 1997), and an importable Python library for use on any binary matrix.

References

Gray, Russell D., David Bryant, and Simon J. Greenhill. 2010. “On the shape and fabric of human history.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (1559): 3923–33. doi:10.1098/rstb.2010.0162.

Holland, Barbara R, K T Huber, A Dress, and V Moulton. 2002. “[delta] Plots: A tool for analyzing phylogenetic distance data.” Molecular Biology and Evolution 19 (12): 2051–9. http://mbe.oxfordjournals.org/content/19/12/2051.full.

Maddison, D R, D L Swofford, and Wayne P. Maddison. 1997. “Nexus: An extensible file format for systematic information.” Systematic Biology 46 (4): 590–621.