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    70 repositories

    • BATH

      Public
      Better Alignments with Translated HMMER
      bioinformaticshidden-markov-modelsframeshifts
      C
      •
      Other
      •4•24•1•0•Updated Jan 19, 2026Jan 19, 2026

    • aurora

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Jan 17, 2026Jan 17, 2026

    • nail-benchmarks

      Public
      A collection of reproducible benchmarks for nail
      Python
      •0•0•0•0•Updated Jan 15, 2026Jan 15, 2026

    • mdr

      Public
      MDRepo tools in Rust
      Dockerfile
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 14, 2026Jan 14, 2026

    • MiRROR

      Public
      Masses in Reflection Reveal Ordered Residues
      proteomicsmass-spectrometrypeptide-sequencingde-novo-peptide-sequencing
      Python
      •0•0•0•0•Updated Jan 13, 2026Jan 13, 2026

    • nail

      Public
      Nail is an Alignment Inference tooL
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •3•55•0•0•Updated Jan 12, 2026Jan 12, 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

    • sculu-rs

      Public
      Rust implementation of SCULU (Subfamily Clustering Using Label Uncertainty)
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 10, 2025Dec 10, 2025

    • 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

    • DIPLOMAT

      Public
      Deep learning-based Identity Preserving Labeled-Object Multi-Animal Tracking (Beta)
      machine-learningdeep-learning
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•8•1•0•Updated Nov 8, 2025Nov 8, 2025

    • ULTRA

      Public
      ULTRA Locates Tandemly Repetitive Areas
      bioinformaticstandem-repeats
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •5•40•2•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 https://github.com/georgeglidden/sufr/
      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 into alignments.
      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
      bioinformaticsalgorithmlcpsuffix-array
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •2•26•3•1•Updated May 2, 2025May 2, 2025

    • 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
      •3.1k•0•0•0•Updated Apr 29, 2025Apr 29, 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
      benchmarkalignmentpalindromeproteomicspalindromessequence-alignmentfalse-positivereversaldecoydecoys
      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
      •3•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-structuresfm-index
      C
      •
      BSD 3-Clause "New" or "Revised" License
      •5•36•0•0•Updated Dec 9, 2024Dec 9, 2024

    • release-workflow-example

      Public
      Example of tags triggering github actions to create releases
      C
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 20, 2024Nov 20, 2024

    • ULTRA-paper

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Nov 15, 2024Nov 15, 2024

    • geomxrename

      Public
      Rename files for use by GeoMX NGS Pipeline app on BaseSpace (Illumina)
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 13, 2024Nov 13, 2024

    • NINJA

      Public
      Nearly Infinite Neighbor Joining Application
      C
      •
      MIT License
      •6•5•19•0•Updated Sep 10, 2024Sep 10, 2024