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.

File conversion scripts for DNA sequence data

MBEToolbox: Matlab toolbox for molecular evolution

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

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

A nextflow pipeline which executes treemix on a population of interest

Repository with Phylip 3.697 with binaries for Apple Silicon

One-stop phylogenetic workflow for protein and DNA/CDS with CLI batch runs, Java GUI interactive parameter tuning, tree inference, summary heatmaps, and tanglegram comparison.

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

Preserving, mining, and modernizing PHYLIP's algorithmic legacy — 35,805 lines of Rust, 1,050 tests, zero dependencies

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