Repositories list

• wikijs

  Public
  Wiki.js | A modern and powerful wiki app built on Node.js | Wheeler Lab fork

  Vue

  •

  GNU Affero General Public License v3.0

  •3.2k•0•0•0•Updated Mar 25, 2026Mar 25, 2026

• mdrepo-rs

  Public
  MDRepo tools in Rust

  Rust

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Mar 24, 2026Mar 24, 2026

• nail-benchmarks

  Public
  A collection of reproducible benchmarks for nail

  Python

  •0•0•0•0•Updated Mar 23, 2026Mar 23, 2026

• nail

  Public
  Nail is an Alignment Inference tooL

  Rust

  •

  BSD 3-Clause "New" or "Revised" License

  •3•54•0•0•Updated Mar 23, 2026Mar 23, 2026

• BLIMMP

  Public
  Python

  •1•0•0•0•Updated Mar 23, 2026Mar 23, 2026

• aurora

  Public
  Rust

  •

  BSD 3-Clause "New" or "Revised" License

  •0•2•0•0•Updated Mar 19, 2026Mar 19, 2026

• sculu

  Public
  Rust implementation of SCULU (Subfamily Clustering Using Label Uncertainty)

  Rust

  •

  BSD 3-Clause "New" or "Revised" License

  •0•2•0•0•Updated Mar 16, 2026Mar 16, 2026

• BATH-paper

  Public
  C

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Mar 16, 2026Mar 16, 2026

• BATH

  Public
  Better Alignments with Translated HMMER

  bioinformaticshidden-markov-modelsframeshifts

  bioinformaticshidden-markov-modelsframeshifts

  C

  •

  Other

  •5•25•1•0•Updated Mar 10, 2026Mar 10, 2026

• DIPLOMAT

  Public
  Deep learning-based Identity Preserving Labeled-Object Multi-Animal Tracking (Beta)

  machine-learningdeep-learning

  machine-learningdeep-learning

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •3•8•1•0•Updated Mar 5, 2026Mar 5, 2026

• DCR-project

  Public
  Code and Data supporting the Dual Coding Region paper

  R

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Feb 25, 2026Feb 25, 2026

• long-range-interactions

  Public
  predicting stability of residue mutations from long range interaction data.

  Python

  •0•0•0•0•Updated Feb 23, 2026Feb 23, 2026

• MiRROR

  Public
  Masses in Reflection Reveal Ordered Residues

  proteomicsmass-spectrometrypeptide-sequencing+ 1

  proteomicsmass-spectrometrypeptide-sequencingde-novo-peptide-sequencing

  Python

  •0•0•0•0•Updated Jan 27, 2026Jan 27, 2026

• Simpatico

  Public
  'Simpatico' is the working title for our GNN which uses contrastive learning to produce co-localized embeddings of compatible protein/ligand atoms.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Jan 7, 2026Jan 7, 2026

• stk2fasta

  Public
  Split Stockholm file into FASTA files

  Rust

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•0•0•Updated Dec 9, 2025Dec 9, 2025

• ULTRA

  Public
  ULTRA Locates Tandemly Repetitive Areas

  bioinformaticstandem-repeats

  bioinformaticstandem-repeats

  C++

  •

  BSD 3-Clause "New" or "Revised" License

  •5•40•3•0•Updated Oct 23, 2025Oct 23, 2025

• mdr-metadata

  Public
  MDRepo TOML parser/validator

  Rust

  •0•0•0•0•Updated Sep 26, 2025Sep 26, 2025

• pylibsufr

  Public
  Python bindings for sufr written in pyo3 and developed using maturin. See also https://github.com/TravisWheelerLab/sufr/. Currently builds from the fork at http…

  Rust

  •0•0•0•0•Updated Sep 4, 2025Sep 4, 2025

• NEAR

  Public
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •0•2•0•0•Updated Aug 26, 2025Aug 26, 2025

• slack-msgs

  Public
  Backup Slack messages

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 7, 2025Aug 7, 2025

• Mirage

  Public
  Mirage generates multiple sequence alignments of proteoforms by mapping sequences back to their coding regions on the genome and then compressing those mappings…

  bioinformaticsbiologyproteoforms

  bioinformaticsbiologyproteoforms

  Perl

  •

  BSD 3-Clause "New" or "Revised" License

  •4•10•0•0•Updated Jun 27, 2025Jun 27, 2025

• sculu-nf

  Public
  Nextflow implementation of SCULU

  Nextflow

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated May 8, 2025May 8, 2025

• sufr

  Public
  Parallel Construction of Suffix Arrays in Rust

  bioinformaticsalgorithmlcp+ 1

  bioinformaticsalgorithmlcpsuffix-array

  Rust

  •

  BSD 3-Clause "New" or "Revised" License

  •2•26•3•1•Updated May 2, 2025May 2, 2025

• seqr

  Public
  FASTX sequence tool

  Rust

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Mar 26, 2025Mar 26, 2025

• danaides

  Public
  Python

  •0•0•0•0•Updated Mar 5, 2025Mar 5, 2025

• WASITAMATchISAW

  Public
  Approximate palindromes lead to overstated false match rates in benchmarks using reversed sequences

  benchmarkalignmentpalindrome+ 10

  benchmarkalignmentpalindromeproteomicspalindromessequence-alignmentfalse-positivereversaldecoydecoys+ 3

  Jupyter Notebook

  •0•0•0•0•Updated Jan 17, 2025Jan 17, 2025

• AWRY

  Public
  Lightning-fast FM-Index library, for the Rust ecosystem.

  Rust

  •

  BSD 3-Clause "New" or "Revised" License

  •4•0•0•0•Updated Jan 14, 2025Jan 14, 2025

• sufr_benchmarks

  Public
  Benchmarks for libsufr and other suffix array tools

  Shell

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Jan 6, 2025Jan 6, 2025

• strobemers

  Public
  Strobemers in Rust

  Rust

  •

  BSD 3-Clause "New" or "Revised" License

  •0•2•0•0•Updated Dec 28, 2024Dec 28, 2024

• AvxWindowFmIndex

  Public
  A fast, AVX2 and ARM Neon accelerated FM index library

  cbioinformaticsdata-structures+ 1

  cbioinformaticsdata-structuresfm-index

  C

  •

  BSD 3-Clause "New" or "Revised" License

  •5•36•0•0•Updated Dec 9, 2024Dec 9, 2024