Julia package PhyNEST: Phylogenetic Network Estimation using SiTe patterns can:
- Read multi-locus sequence alignment (in a relaxed PHYLIP format) and parse site pattern frequencies for all permutations of four individuals (i.e., sequences).
- Estimate maximum composite likelihood species network using the parsed site pattern frequencies using hill climbing or simulated annealing heuristic algorithms.
To use PhyNEST, Julia >= v1.7 is recommended. This package was developed in Julia 1.7.2, and has been tested for Julia >= v1.7 in OSX distributions.
To install PhyNEST run the following command in Julia prompt:
julia> using Pkg
julia> Pkg.add("PhyNEST")
or
julia> ] add PhyNEST
Either command installs the package. To check the current version of installed PhyNEST, run the following command:
julia> ] status PhyNEST
Once the installation is complete, load PhyNEST and run function greet() to see if the package has been added to the local machine. A greet message with current time should appear.
julia> using PhyNEST
julia> greet()
Please see here for detailed documentation.
A step-by-step wiki tutorial is available here.
Sungsik Kong, David Swofford, and Laura Kubatko (2022) Inference of Phylogenetic Networks from Sequence Data using Composite Likelihood. Preprint available online on BioRxiv at https://doi.org/10.1101/2022.11.14.516468.
Please use google group to report bugs or make suggestions.