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Starred repositories
Fast, parallel Rust implementation of Prodigal for prokaryotic gene prediction in microbial genomes
Iterative Gene clUster Analysis, a high-throughput method for gene cluster family identification.
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
`thaf` is a command-line tool to extract transcript sequences from a genome FASTA file based on GFF3 annotation files. It can also generate transcript-to-gene mapping files compatible with tools su…
Comparison pipeline for Prokaryote Protein Coding Gene Predictors
add statistical significance annotations on seaborn plots. Further development of statannot, with bugfixes, new features, and a different API.
Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs
base-accurate DNA sequence alignments using WFA and mashmap3
Sparse Neighbor Joining: rapid phylogenetic inference using a sparse distance matrix.
Code, intermediate results and an interactive visualisation on prediction of putative novel enzymes and small molecule binding proteins presented in (Barrio-Hernandez et al. 2023)
Fast protein domain structure embedding+search tool
A lightweight yet powerful audio-to-MIDI converter with pitch bend detection
🛰️ An approximate nearest-neighbor search library for Python and Java with a focus on ease of use, simplicity, and deployability.
Approximate Nearest Neighbors in C++/Python optimized for memory usage and loading/saving to disk
Modeling whole bacterial genome as a sequence of proteins.
Multi-scale and multi-task benchmark for evaluating ML models for bacterial genomics across the bacterial tree of life.
FAPLM: A Drop-in Efficient Pytorch Implementation of Protein Language Models
Generate UniProt-based AlphaFold3 JSON including all annotated post-translational modifications
Compares pangenome graphs by calculating the segmentation distance between two GFA (Graphical Fragment Assembly) files.
Example Python package
Geometric Deep Learning for Prediction of Protein-Carbohydrate Binding Interfaces