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bGMYC4: Package Overview

Dmitry Karabanov

2026-08-24

Overview

The bGMYC4 package implements a Bayesian version of the General Mixed Yule-Coalescent model for species delimitation from single-locus phylogenetic data. It uses Markov Chain Monte Carlo simulation to evaluate the posterior distribution of species boundaries and supports flexible prior specification on model parameters.

Main functions

bgmyc.singlephy() - Bayesian GMYC analysis for a single phylogeny
bgmyc.multiphylo() - Analysis across multiple phylogenies
bgmyc.dataprep() - Prepare data for analysis
plot.singlebgmyc() - Visualize results for a single phylogeny
plot.multibgmyc() - Visualize results across multiple phylogenies

Vignettes

Interactive visualization with bGMYC4 (see bGMYC4-interactive.html)

References

Pons, J., Barraclough, T.G., Gomez-Zurita, J., Cardoso, A., Duran, D.P., Hazell, S., Kamoun, S., Sumlin, W.D., and Vogler, A.P. (2006). Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology, 55(4), 595-609.

Reid, N.M. and Carstens, B.C. (2012). Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model. BMC Evolutionary Biology, 12, 196.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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