Martin Larralde
althonos
PhD candidate in Bioinformatics, passionate about programming, SIMD-enthusiast, Pythonista, Rustacean. I write poems, and sometimes they are executable.
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Top Repositories
Another API-less Instagram pictures and videos downloader. (defunct)
A progress bar for ffmpeg. Yay !
A Python frontend to (Open Biomedical) Ontologies.
Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
Cython bindings and Python interface to HMMER3.
Physicochemical properties, indices and descriptors for amino-acid sequences.
Repositories
90Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
Pure-Python, array-library-agnostic utilities related to Jaccard indices.
Conda recipes for the bioconda channel.
Cython bindings and Python interface to MUSCLE v5, a highly efficient and accurate multiple sequence alignment software.
Dependency free, Cython-compatible scoring matrices to use with biological sequences.
Cython bindings and Python interface to trimAl, a tool for automated alignment trimming. Now with SIMD!
Cython bindings and Python interface to ARAGORN, a (t|mt|tm)RNA gene finder.
Cython bindings and Python interface to Tantan, a fast method for identifying repeats in DNA and protein sequences.
Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.
Cython bindings and Python interface to the MEME suite, a collection of tools for the analysis of sequence motifs.
Cython bindings and Python interface to CoMSA, a compressor for multiple-sequence alignments.
Cython bindings and Python interface to the NCBI C++ ToolKit (including BLAST+).
Cython bindings and Python interface to SWORD (Smith Waterman On Reduced Database), a heuristic method for fast database search.
Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
Cython bindings and Python interface to Jess, a 3D template matching software for protein structures. Now 10x faster!
Another API-less Instagram pictures and videos downloader. (defunct)
Physicochemical properties, indices and descriptors for amino-acid sequences.
A Rust reimplementation of the MinCED method for identifying CRISPRs in full or assembled genomes.
A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.
A NumPy port of the foldseek code for encoding protein structures to 3di.
Trains in 2 company colours (narrow-gauge edition)
A Python frontend to (Open Biomedical) Ontologies.
Cython bindings and Python interface to HMMER3.
Cython bindings and Python interface to Infernal 1.1.
A progress bar for ffmpeg. Yay !
A lightweight platform-accelerated library for biological motif scanning using position weight matrices.
Aim to be the bioinformatics repository with more and newer packages https://doi.org/10.1093/bioinformatics/btaf106
A NumPy port of the NEAR code for embedding protein sequences.
A Python interface to gb-io, a fast GenBank parser written in Rust.
A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.