Martin Larralde

A Python frontend to (Open Biomedical) Ontologies.

A progress bar for ffmpeg. Yay !

Cython bindings and Python interface to HMMER3.

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

Another API-less Instagram pictures and videos downloader. (defunct)

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

Pyfilesystem2 over SSH using paramiko

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

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

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

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

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

Pyfilesystem2 over SMB using pysmb

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

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

Cython bindings and Python interface to MUSCLE v5, a highly efficient and accurate multiple sequence alignment software.

A simple Rust macro to derive blanket implementations for your traits.

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

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

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

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

Pyfilesystem2 for various archive filesystems

Cython bindings and Python interface to the MEME suite, a collection of tools for the analysis of sequence motifs.

A zero-copy file-like wrapper for Python byte buffers, inspired by Rust's std::io::Cursor.

Rust data structures and client for the PubChem REST API

A 10x faster drop-in reimplementation of cksfv using Rust and the crc32fast crate.

Simple procedural macros to use textwrap utilities at compile time.

Modular cloning simulation with the MoClo framework in Python

Cython bindings and Python interface to Jess, a 3D template matching software for protein structures. Now 10x faster!

Cython bindings and Python interface to the NCBI C++ ToolKit (including BLAST+).

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

Cython bindings and Python interface to Infernal 1.1.

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

A GreaseMonkey userscript to add a Full Text Link button redirecting to Sci-Hub on PubMed article pages.

Rust data structures and parser for the Uniprot database(s).

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

A PyTorch implementation of Tree-structured Conditional Random Fields.

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

A small thunar extension displaying the metadata in a torrent file.

A Jinja2 template loader using PyFilesystem2.

A memory-optimized wrapper for Python sets likely to be empty.

No description.

A (better) decorator for caching properties in classes (forked from cached-property).

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

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

A PPSSPP texture pack for La Pucelle Ragnarok (english patched)

Rust bindings to Flips, the Floating IPS patcher.

Redundancy checks in pure Rust

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

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

Read optical media filesystems with Rust

Chemical structure generation for protein sequences as SMILES string.

The PICO-8 font to use with embedded-graphics.

Pure Python port and interface to ABRicate, a tool for mass screening of contigs for antimicrobial resistance or virulence genes.

A hidden conditional random field (HCRF) implementation in Python.

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

A toy compiler that produces Kappa code from Counter Machine instructions.

Python Sorted Container Types: Sorted List, Sorted Dict, and Sorted Set

A Snakemake pipeline to copy annotations between GenBank files

An experimental patch with fixed-point arithmetic support for Lua 5.3

Trains in 2 company colours (narrow-gauge edition)

Structures to deserialize OBO Foundry listings into.

Pure-Python, array-library-agnostic utilities related to Jaccard indices.

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

Detect transcription factor binding sites in bacterial genomes

Not the slurm job dispatcher you need, but the one you deserve.

8-bit badges for OpenTTD 15.0 and later

OpenTTD is an open source simulation game based upon Transport Tycoon Deluxe

antiSMASH

A Platform-Accelerated Package for Alignment-free SMURF analysis.

Conda recipes for the bioconda channel.

Aim to be the bioinformatics repository with more and newer packages https://doi.org/10.1093/bioinformatics/btaf106

HMMER: biological sequence analysis using profile HMMs

Cython bindings and Python interface to PhyML 3.

No description.

No description.

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

Rust parser combinator framework

My own configuration files for the fish shell

💥 Fast matrix-multiplication as a self-contained Python library – no system dependencies!

information artifact ontology

No description.

High level Lua bindings to Rust (with fixed-point arithmetic support)

GUI for monitoring NVIDIA GPU (adapted from bbswitch-gui)

Fast hierarchical agglomerative clustering in Rust.

Prodigal Gene Prediction Software

SIMD C/C++ library for massive optimal sequence alignment (local/SW, infix, overlap, global)

Multiple sequence alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.

Sphinx Bootstrap Theme

Benchmarking different languages for a simple bioinformatics task (Counting the GC fraction of DNA in a FASTA file)

A minimal webapp to display Botrytis cinerea sequencing data using CherryPy, Jinja2 and Bootstrap

No description.

Some anime logos I remade myself in vector graphics

Quick and dirty CLI app to backup an eLabFTW instance using the HTTP API