Python code to color a PDB structure based on parameters from a multiple sequence alignment

Script for removing or counting invariant sites for the RAxML ascertainment bias corrections

Automated pipeline for whole bacterial genome analysis based on snakemake

Phylogeographic workflow using sliding-windows, RAxML-NG and FastTree

snpick is a fast and memory-efficient Rust-based SNP extraction tool designed to handle large genomic alignments with minimal RAM usage and high-speed performance.

Shell script pipeline for inferring ML gene trees for many loci (e.g. genomic RAD loci)

Commonly used phylogenetic methods, Monash HPC access and basic bioinformatics

RAxML pipeline

Program to generate RAxML sliding window trees

Data and scripts to reproduce the molecular clock dating analyses presented in "Ancient bacterial genomes reveal a formerly unknown diversity of Treponema pallidum strains in early modern Europe (Majander et al.)