iqtree

Reference-based consensus creation

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.

Auditable agent skill for resolving protein queries, selecting references, and planning reproducible phylogenetic trees.

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

A transparent ONT bacterial assembly case study for an *Acinetobacter* barcode07 isolate, built not only to generate an assembly, but to show how raw reads become an interpretable genome through QC evidence, assembler comparison, graph checks, phylogeny, annotation, documented decisions, and honest limitations.

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.

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

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 reproducible bioinformatics pipeline for variant calling and phylogenetic analysis of ancient Streptococcus mutans genomes.

Reproducible core-SNP phylogenetic pipeline for public E. coli genomes using Snippy, IQ-TREE, Biopython, SQLite, and metadata-linked visualization.

Exploring how gene families vary across E. coli strains using comparative genomics, phylogenetic analysis, and functional annotation.

MCP server for phylogenetic inference over IQ-TREE 2 — never returns a topology without its bootstrap support

A Nextflow pipeline to generate a phylogenetic tree from SKA alignment

Comparative phylogenetic inference in Capsicum: alignment-free MinHash distances vs. alignment-based transcriptome assemblies (course write-up, 2025)