Software

Topology weighting by iterative sorting of sub-trees

This method quantifies relationships between taxa that are not-necessarily monophyletic by counting the occurrence of different sub-tree topologies.

Twisst2 is ready for testing. It improves on the method by including inference of trees and their breakpoints along the genome. Give it a try!

I maintain a collection of scripts for manipulation and analysis of genomic data

Parse VCF files, compute statistics like F_ST and f_d in sliding windows etc.

R functions for visualising genome alignments

Make dot plots or alignment plots. Identify synteny blocks.