Most softwares and scripts are available on github. The most important softwares are briefly described below...
© Simon Joly, 2011-2013Montreal Botanical Garden
JML is a program that implements the posterior predictive checking method of Joly et al. 2009 for detecting hybridization events. Replicate datasets are simulated from the posterior distribution of species trees (with branch lengths and population sizes) using the coalescent. Then a test quantity, the minimum distance between sequences of two species, is calculated for all replicated datsets to generate a posterior predictive distribution. The observed distance is finally compared to this distribution to calculate the probability that the observed distance is caused by hybridization.
Source code and binaries for the program are available on Github
Joly, S. 2012. JML: Testing hybridization from species trees. Molecular Ecology Ressources. 12:179-184
Joly, S., P.A. McLenachan, P.J. Lockhart. 2009. A statistical approach for distinguishing hybridization and incomplete lineage sorting. The American Naturalist 174: e54-e70
© Simon Joly, 2006-2014
Montreal Botanical Garden
POFAD implements several approaches for estimating genetic distances between individuals (organisms) in the presence of intra-individual polymorphisms or SNPs due to allelic variation, polyploidy, gene families, etc. Read the manual for further information.
Source code and binaries for the program are available on Github
Joly, S. and Bruneau. 2006. Incorporating allelic variation for reconstructing the evolutionary history of organisms from multiple genes: an example from Rosa in North America. Systematic Biology. 55(4):623-636.
Joly, S. D. Bryant, and P. J. Lockhart. 2015. Flexible methods for estimating genetic distances from nucleotide data. Methods in Ecology and Evolution. 6(8):938-948