Uses a hidden markov to assign a species tree to each loci in data coming from a species network.
Before using this command, you need to get lib.zip. Assuming it is then unzipped to LocalPath where the unzipped folder is located,
- Mac: use -Djava.library.path=LocalPath/lib, when launching PhyloNet from command line.
- Linux: add LocalPath/lib to your LD_LIBRARY_PATH, before launching PhyloNet from command line.
- Windows: please contact us.
The species network topology of the data. Branch lengths are not needed.
Changes the mutation model from the default JC to GTR.
Gene tree / species network taxa association.
The number of hill climbing iterations to use for each run.
The number of threads to use when processing.
The number of times to restart the hill climbing process.
Stop showing plots when finished.
The directory to store the output of the run.
Liu KJ, Dai J, Truong K, Song Y, Kohn MH, and Nakhleh L (2014) An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes. PLoS Comput Biol 10(6): e1003649.
Liu KJ, Steinberg E, Yozzo A, Song Y, Kohn MH, and Nakhleh L (2014) Interspecific Introgressive Origin of Genomic Diversity in the House Mouse. Under review.