Explore projects

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

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.

This is meant as a playground for learning some basics in version control and code collaboration.

Various tools operating over VCF files. Uses cyvcf2 and cython under the hood for speed

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

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

A PyTorch implementation of Tree-structured Conditional Random Fields.

RNA-seq pipeline for AML diagnostics. Illustration from Anatomy & Physiology, licenced under the Creative Commons Attribution 3.0 Unported

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

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