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    32 repositories

    • cactus

      Public
      Official home of genome aligner based upon notion of Cactus graphs
      C
      •
      Other
      •123•649•563•8•Updated Feb 3, 2026Feb 3, 2026

    • paffy

      Public
      Small C/CLI library of pairwise alignment format (paf) format tools used by Cactus
      C
      •2•6•2•0•Updated Feb 1, 2026Feb 1, 2026

    • hal

      Public
      Hierarchical Alignment Format
      C++
      •
      Other
      •39•174•108•0•Updated Jan 23, 2026Jan 23, 2026

    • taffy

      Public
      This is a library C/Python/CLI for working with TAF (.taf,.taf.gz) and MAF (.maf) alignment files
      C
      •
      MIT License
      •3•29•11•2•Updated Aug 26, 2025Aug 26, 2025

    • cactus-gfa-tools

      Public
      C++
      •
      MIT License
      •1•2•2•0•Updated Aug 21, 2025Aug 21, 2025

    • mafTools

      Public
      Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.
      C
      •
      Other
      •32•11•0•0•Updated Jul 8, 2025Jul 8, 2025

    • matchingAndOrdering

      Public
      Library of matching and ordering algorithms, used for the "reference problem"
      C
      •1•1•0•0•Updated Jul 3, 2025Jul 3, 2025

    • cPecan

      Public
      C + python code for pairwise multiple sequence alignment, pulling out this functionality from the Cactus alignment program.
      C
      •
      MIT License
      •12•0•0•1•Updated Jul 3, 2025Jul 3, 2025

    • Comparative-Annotation-Toolkit

      Public
      Python
      •
      Apache License 2.0
      •48•186•112•4•Updated May 22, 2025May 22, 2025

    • sonLib

      Public
      Small general-purpose library for C and Python with an emphasis on bioinformatics.
      C
      •
      MIT License
      •4•8•4•4•Updated May 1, 2025May 1, 2025

    • hal2vg

      Public
      Convert HAL to VG
      C++
      •
      MIT License
      •2•23•7•0•Updated Aug 12, 2024Aug 12, 2024

    • cactus2hal

      Public
      C++
      •1•0•0•0•Updated Jul 17, 2024Jul 17, 2024

    • RetroFinder

      Public
      Tool for finding retroposed genes in genomes
      C
      •
      MIT License
      •0•1•0•0•Updated Apr 6, 2024Apr 6, 2024

    • maf_stream

      Public
      Rust
      •1•0•0•0•Updated Jun 20, 2023Jun 20, 2023

    • cactusTestData

      Public
      Datasets required to run cactus unit tests
      1•0•0•0•Updated Jun 5, 2023Jun 5, 2023

    • SegAlign

      Public
      A Scalable GPU System for Pairwise Whole Genome Alignments
      C++
      •
      MIT License
      •16•3•0•0•Updated Jun 5, 2023Jun 5, 2023

    • lastz

      Public
      Program for aligning DNA sequences, a pairwise aligner.
      C
      •
      MIT License
      •41•1•0•0•Updated Apr 4, 2023Apr 4, 2023

    • 363-avian-2020-hub

      Public
      Assembly hub for 363-way avian alignment from 2020
      HTML
      •0•0•0•0•Updated Apr 4, 2023Apr 4, 2023

    • zoonomia-hub

      Public
      Zoonomia hub
      HTML
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 3, 2023Apr 3, 2023

    • abPOA

      Public
      abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
      C
      •
      MIT License
      •20•0•0•1•Updated Dec 12, 2022Dec 12, 2022

    • repeatMaskerPipeline

      Public
      Python
      •3•0•0•0•Updated Oct 4, 2022Oct 4, 2022

    • ComparativeGenomicsToolkit.github.io

      Public
      HTML
      •0•1•0•0•Updated Sep 27, 2022Sep 27, 2022

    • pinchesAndCacti

      Public
      Library for constructing pinch graphs and cactus graphs
      C
      •1•2•0•0•Updated Jul 1, 2021Jul 1, 2021

    • kyoto

      Public
      Kyoto Tycoon key-value store (and the underlying Kyoto Cabinet library)
      C++
      •
      GNU General Public License v3.0
      •42•1•0•1•Updated Apr 7, 2020Apr 7, 2020

    • neutral-model-estimator

      Public
      Simple pipeline to go from an alignment to a neutral model, using the PHAST toolkit
      Python
      •
      MIT License
      •1•11•2•0•Updated Jan 17, 2020Jan 17, 2020

    • toil

      Public
      A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python
      Python
      •
      Other
      •245•0•0•0•Updated Jan 8, 2019Jan 8, 2019

    • hal-grpc-server

      Public
      C++
      •
      Other
      •0•0•0•0•Updated Nov 18, 2018Nov 18, 2018

    • CAT_paper

      Public
      TeX
      •1•0•0•0•Updated May 2, 2018May 2, 2018

    • quick-tree-check

      Public
      Fast phylogeny estimation/verification using alignment-free distances.
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 13, 2018Mar 13, 2018

    • alignment-annotation-review

      Public
      TeX
      •0•0•0•0•Updated Dec 12, 2017Dec 12, 2017