Java source code and executables for software associated with several of my publications is available on github. Instructions for running the software will be given for each project – email me if these are not posted yet.
GATSby is required to run all my other software. It provides a very wide variety of structures and methods for phylogenetic trees. Most importantly, it combines representations of trees as (a) graph structures (sets of vertices and edges) and (b) as weighted sets of compatible splits. The former representation allows efficient representation of Markov substitutions on trees and associated probability calculations (simulating alignments, calculating likelihoods); the latter representation is the best for analysis of trees in Billera-Holmes-Vogtmann (BHV) tree space. The libraries include methods to swap between these representations. It is possibly unique in proividing this combination of representations. Features include:
Compare2Trees is a popular program for comparing phylogenetic trees. It is showing its age now as it was first published in 2006. In order to run the executable, you need to download the Compare2Trees jar files and those for GATSby.
GeoPhytter fits geodesics and higher-dimensional surfaces to data in BHV tree space. It provides methodology associated with three of my publications for tree space PCA:
ProbDist uses simulation methods to compute probabilistic distances between phylogenetic trees. It provides methodology associated with my paper on probabilistic distances between trees, Systematic Biology, 2018.