Example - sungsik-kong/PhyNEST.jl GitHub Wiki

An example PHYLIP sequence alignment is located in PhyNEST.jl.wiki/example-data with the file name sample_n5h1.phy. This is a simulated dataset that contains five sequences, including an outgroup. Each sequence represents a discrete species and are named as outgroup, species_1, species_2, species_3, and species_4. The alignment is 1 million base pairs (bp) long, composed of 4000 loci, each of which is 250 bp long.

Take a look at the dimensionality of the data by printing the first line of the alignment:

head -n1 sample_n5h1.phy
5 1000000

Open julia and load PhyNEST:

julia> using PhyNEST

Execute the function greet() to make sure PhyNEST is loaded correctly. greet() prints the address for Google group where users can report bugs and make suggestions, as well as how to cite PhyNEST.

julia> greet()

julia> using PhyNEST
julia> greet()
Thank you for using PhyNEST: Phylogenetic Network Estimation using SiTe patterns (current time: 2023-06-18T14:59:14.416).
Please report bugs or make suggestions to https://groups.google.com/g/phynest-users.
If you conduct an analysis using PhyNEST, please cite:
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.

Next: Parsing input data