Compute a pairwise SNP distance matrix from one or two alignment(s)

Read alignment statistics for metagenomics

More scalable dereplication for metagenome assembled genomes

Simple terminal alignment viewer

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

Cross-platform software to draw phylogenetic trees

Find clustered hits from a BLAST search

Build a partitioned pangenome graph from microbial genomes

Hidden Markov Model profile reader/writer

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

Efficient pythonic random access to fasta subsequences

Building the compacted de Bruijn graph efficiently from references or reads.

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

A Rich renderable for viewing Multiple Sequence Alignments in the terminal.

🧬 Efficient parallelized peta-scale protein database search

Assessing the quality of metagenome-derived genome bins using machine learning

Viroid-like circRNA discovery and analysis suite

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

Recombination-free trees

Efficient calculation of phylogenetic distance matrices.

Download FASTQ files from SRA or ENA repositories.

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches

Python bindings to bwa mem

Rust bindings to minimap2 library

Discovery of conserved gene clusters in multiple genomes

Precise host read removal