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- Co-estimation of reticulate phylogenies (ILS & hybridization), gene trees, divergence times and population sizes on sequences from multiple independent loci.
- For species phylogeny or phylogenetic network, we infer network topology, divergence times in units of expected number of mutations per site, population sizes in units of population mutation rate per site, and inheritance probabilities.
- For gene trees, we infer gene tree topology and coalescent times in units of expected number of mutations per site.
- To convert the divergence times/coalescent times to units of years, or to coalescent units, see our paper for details (Page 3, Lines 36-43).
- We use BEAGLE, a high-performance library to calculate the "Felsenstein Likelihood". Full details of installation instructions can be found here, always follow "Installing from source".
If there is error, try command: java -Djava.library.path="/usr/local/lib” lib" -jar PhyloNet_X.X.X.jar script.nex
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