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    67 repositories

    • BATH

      Public
      Better Alignments with Translated HMMER
      bioinformaticshidden-markov-modelsframeshifts
      C
      •
      Other
      •4•21•0•0•Updated Jun 19, 2025Jun 19, 2025

    • nail

      Public
      Nail is an Alignment Inference tooL
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •3•48•0•0•Updated Jun 19, 2025Jun 19, 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•7•3•1•Updated Jun 12, 2025Jun 12, 2025

    • MiRROR

      Public
      Masses in Reflection Reveal Ordered Residues
      proteomicsmass-spectrometrypeptide-sequencingde-novo-peptide-sequencing
      Python
      •0•0•0•0•Updated Jun 10, 2025Jun 10, 2025

    • aurora

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Jun 9, 2025Jun 9, 2025

    • NEAR

      Public
      Jupyter Notebook
      •0•2•0•0•Updated Jun 8, 2025Jun 8, 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.
      biologyproteoformsbioinformatics
      Perl
      •
      BSD 3-Clause "New" or "Revised" License
      •4•10•0•0•Updated May 22, 2025May 22, 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

    • ULTRA

      Public
      ULTRA Locates Tandemly Repetitive Areas
      bioinformaticstandem-repeats
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •4•28•2•0•Updated May 5, 2025May 5, 2025

    • sufr

      Public
      Parallel Construction of Suffix Arrays in Rust
      bioinformaticsalgorithmlcpsuffix-array
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •2•23•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
      •3k•0•0•0•Updated Apr 29, 2025Apr 29, 2025

    • 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 Apr 22, 2025Apr 22, 2025

    • pylibsufr

      Public
      Python bindings for sufr written in pyo3 and developed using maturin. See also https://github.com/TravisWheelerLab/sufr/
      Rust
      •0•0•0•0•Updated Mar 31, 2025Mar 31, 2025

    • seqr

      Public
      FASTX sequence tool
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Mar 26, 2025Mar 26, 2025

    • stk2fasta

      Public
      Split Stockholm file into FASTA files
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Mar 25, 2025Mar 25, 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

    • nail-benchmarks

      Public
      A collection of reproducible benchmarks for nail
      Python
      •0•0•0•0•Updated Jan 15, 2025Jan 15, 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•32•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
      •7•5•19•0•Updated Sep 10, 2024Sep 10, 2024

    • nailforge

      Public
      a fast and sensitive nucleotide and protein sequence homology prefilter
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Aug 7, 2024Aug 7, 2024

    • face

      Public
      Processing FAISS hits with Python/Rust
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jul 12, 2024Jul 12, 2024

    • tallyman

      Public
      Tallyman helps you count sequence occurrences
      Jupyter Notebook
      •1•0•14•6•Updated Jun 28, 2024Jun 28, 2024

    • easel

      Public
      Sequence analysis library used by Eddy/Rivas lab code
      C
      •
      Other
      •29•0•0•0•Updated Jun 25, 2024Jun 25, 2024