althonos

pronto

A Python frontend to (Open Biomedical) Ontologies.

pyrodigal

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

pyhmmer

Cython bindings and Python interface to HMMER3.

peptides.py

Physicochemical properties, indices and descriptors for amino-acid sequences.

lightmotif

A lightweight platform-accelerated library for biological motif scanning using position weight matrices.

mini3di

A NumPy port of the foldseek code for encoding protein structures to 3di.

pyfamsa

Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.

pyskani

PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.

pyfastani

Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.

pytrimal

Cython bindings and Python interface to trimAl, a tool for automated alignment trimming. Now with SIMD!

orthoani

A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.

pysylph

PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.

gb-io.py

A Python interface to gb-io, a fast GenBank parser written in Rust.

pyrodigal-gv

A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.

pyopal

Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.

packageurl.rs

Rust implementation of the Package URL specification.

scoring-matrices

Dependency free, Cython-compatible scoring matrices to use with biological sequences.

pyjess

Cython bindings and Python interface to Jess, a 3D template matching software for protein structures.

nafcodec

Rust coder/decoder for Nucleotide Archival Format (NAF) files.

pyswrd

Cython bindings and Python interface to SWORD (Smith Waterman On Reduced Database), a heuristic method for fast database search.

diced

A Rust reimplementation of the MinCED method for identifying CRISPRs in full or assembled genomes.

MiniMotif

Detect transcription factor binding sites in bacterial genomes

pytantan

Cython bindings and Python interface to Tantan, a fast method for identifying repeats in DNA and protein sequences.

rlinalg

Linear Algebra routines for Python as implemented in the R language.

2ccng

Trains in 2 company colours (narrow-gauge edition)

bioconda-recipes

Conda recipes for the bioconda channel.

config.fish

My own configuration files for the fish shell

horned-owl

obofoundry.rs

Structures to deserialize OBO Foundry listings into.

sylph

ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.