JolyTree is a script that implements an alignment-ƒree distance-based procedure ƒor inferring phylogenetic trees ƒrom genome contig sequences. For each pair of genomes, a dissimilarity measure is ƒirst computed and next transƒormed to obtain an estimation oƒ the number oƒ substitution events that have occurred during their evolution. These pairwise evolutionary distances are then used to inƒer a phylogenetic tree and assess a conƒidence support ƒor each internal branch. Analyses oƒ both simulated and real genome datasets have shown that JolyTree allows accurate phylogenetic trees to be reconstructed with ƒast running times, especially when launched on multiple threads.
JolyTree is ƒreely available at gitlab.pasteur.fr/GIPhy/JolyTree. It runs on UNIX, Linux and most OS X operating systems.