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A collection of semi-reusable scripts, which are not part of any official toolchain

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

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

Mirror of https://github.com/LOVDnl/LOVD3.git

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

3D Ultrasound

Cython bindings and Python interface to CoMSA, a compressor for multiple-sequence alignments.

Physicochemical properties and indices for amino-acid sequences (ported from R).

A NumPy port of the NEAR code for embedding protein sequences.

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

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

Cython bindings and Python interface to ARAGORN, a (t|mt|tm)RNA gene finder.

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes.

Repository containing a Snakemake ChIPseq pipeline for SE and PE datasets

Repository for Jianhui's snakemake pipeline