PhyloNet-HMM consists of a statistical model and associated inference method for analyzing complex evolutionary scenarios, especially non-tree-like evolutionary scenarios. PhyloNet-HMM combines phylogenetic networks, which capture complex evolutionary relationships among genomes, with hidden Markov models, which capture dependencies within genomes, in a novel manner. The performance of PhyloNet-HMM was validated using simulated and empirical data sets that included tree-like and non-tree-like evolutionary scenarios. A detailed description of the model, inference method, and performance study is available in the following manuscript: 

K. Liu, J. Dai, K. Truong, Y. Song, M. H. Kohn, and L. Nakhleh, "An HMM-based comparative genomic framework for detecting introgression in eukaryotes," PLoS Computational Biology, vol. 10, no. 6, p. e1003649, 2014, doi: 10.1371/journal.pcbi.1003649.

Software and data sets are provided below as compressed tarball files. See README file in each compressed tarball file for a detailed explanation of contents.

PhyloNet-HMM is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. PhyloNet-HMM is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with PhyloNet-HMM.  If not, see <>.