Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. 2014 but using DIAMOND instead of BLASTP for alignments.

Workflow for AnnoView upload

Super snazzy online phylogenetic tree viewer with automatic customization using simple, tab-separated text files.

all methods related to Enterobase

An R package designed for drawing gene arrow maps

R package for microbial pangenomics

PanTools

A quality control pipeline for PanTools input data

General purpose Snakemake pipeline for PanTools v4.

ggplot extension: options for tailored facets, multiple colourscales and miscellaneous

Biological sequence clustering tool with dynamic threshold

Utility to analyse a group of closely related MAgs/Genomes/bins/SUBs of more or less dubious origin

The gview wiki migrated to GitHub.

💔 An implementation of scale functions for setting axis breaks of a 'gg' plot.

oxford dot plots

a tool to filter sites in a FASTA-format whole-genome pseudo-alignment

A growing collection of bioinformatics tutorials, project guides, tools, and articles I’ve developed to make bioinformatics more accessible.

AI Crash Course to help busy builders catch up to the public frontier of AI research in 2 weeks

Mumemto: multi-MUM and MEM finding across pangenomes

📚 Various bioinformatics tutorials

A pipeline for analyzing bacterial genomic sequences. Easily.

MMseqs2: ultra fast and sensitive search and clustering suite

Phylogenetic orthology inference for comparative genomics

Lecture notes for EC 607

A grammar of graphics for comparative genomics

The simplest, fastest repository for training/finetuning medium-sized GPTs.

LexicMap: efficient sequence alignment against millions of prokaryotic genomes

forester is a collection of open source libraries of Java and Ruby software for phylogenomics and evolutionary biology research