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.

Implementation of PsiPartition: Improved Site Partitioning for Genomic Data by Parameterized Sorting Indices and Bayesian Optimization

A reproducible Snakemake pipeline for the high-throughput genomic epidemiology of 96 MDR P. aeruginosa strains (BioProject PRJNA771342).

This repository provides a comprehensive tutorial for phylogenetic analysis, covering data collection, sequence alignment, tree construction, and interpretation. It runs on AWS SageMaker using Jupyter notebooks and includes tools like MAFFT, Nextclade, and IQ-TREE.

GUI and CLI workflow for phylogenetic tree construction, tanglegram comparison, and optional Foldseek protein-structure similarity.

An automated phylogenomics workflow that utilizes GToTree for marker gene extraction and IQ-Tree for high-resolution Maximum Likelihood tree inference.

A Nextflow pipeline to generate a phylogenetic tree from SKA alignment

Automated maximum-likelihood phylogeny pipeline for viral families. Discovers species via NCBI Taxonomy, downloads from GenBank, aligns with MAFFT, builds trees with FastTree (broad) and IQ-TREE (refined), and annotates internal nodes by LCA. Supports multi-marker concatenation for large DNA virus families.