PhyNEST.jl

Overview

Julia package PhyNEST.jl: 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.

Installation of the package PhyNEST

To use PhyNEST.jl, 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.jl run the following command in Julia prompt:

using Pkg
Pkg.add("PhyNEST")

or

] add PhyNEST

Either command installs the package. To check the current version of installed PhyNEST.jl, run the following command:

] status PhyNEST

Test example

Once the installation is complete, load PhyNEST.jl and run function greet() to see if the package has been added to the local machine. A greet message with current time should appear.

using PhyNEST
greet()

Documentation

Please see here for detailed documentation.

Getting help

Please use google group to report bugs or make suggestions.