Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

Goalign is a set of command line tools and an API to manipulate multiple sequence alignments. It is implemented in Go language.

MBEToolbox: Matlab toolbox for molecular evolution

File conversion scripts for DNA sequence data

Python script to generate .snp and .ind Eigenstrat files from a PHYLIP infile

API to read, write, and filter DNA sequence alignment files

A nextflow pipeline which executes treemix on a population of interest

Easy Manipulation of Multiple Sequence Alignments (Concatenation and Format Conversion)

Python script to add population identifiers to STRUCTURE, PLINK, and PHYLIP files

Repository with Phylip 3.697 with binaries for Apple Silicon