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    67 repositories

    • cpm2025

      Public
      Combinatorial Pattern Matching 2025
      HTML
      •
      GNU General Public License v2.0
      •0•2•0•0•Updated Sep 23, 2024Sep 23, 2024

    • pangeblocks

      Public
      pangenome from maximal blocks in an MSA
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•9•1•1•Updated Sep 17, 2024Sep 17, 2024

    • galig

      Public
      A graph aligner
      Python
      •
      GNU General Public License v3.0
      •12•26•8•0•Updated Sep 17, 2024Sep 17, 2024

    • pantas

      Public
      Differential quantification of alternative splicing events on spliced pangenome graphs
      Python
      •0•6•0•0•Updated Sep 11, 2024Sep 11, 2024

    • RecGraph-exps

      Public
      Python
      •0•0•0•0•Updated Jul 17, 2024Jul 17, 2024

    • RecGraph

      Public
      Optimal sequence-to-graph alignment with recombinations
      alignmentpoapangenomicsrust
      Rust
      •
      MIT License
      •2•24•3•0•Updated Jul 11, 2024Jul 11, 2024

    • complexCGR

      Public
      complex Chaos Game Representation for DNA sequences
      Python
      •
      MIT License
      •0•14•0•0•Updated Mar 26, 2024Mar 26, 2024

    • COPA24

      Public
      PhD school on Evolution in Computational Pangenomics
      MIT License
      •60•0•0•0•Updated Feb 14, 2024Feb 14, 2024

    • materiale-stage-tesi

      Public
      Una raccolta di materiale utile per tutti gli studenti che iniziano a lavorare
      Rust
      •
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Jan 31, 2024Jan 31, 2024

    • rs-gax

      Public
      Rust
      •1•0•0•0•Updated Dec 2, 2023Dec 2, 2023

    • ESGq

      Public
      Python
      •0•2•0•0•Updated Jul 1, 2023Jul 1, 2023

    • meta_cancer

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Jun 27, 2023Jun 27, 2023

    • LightStringGraph

      Public
      Lightweight String Graph Construction
      C++
      •
      GNU General Public License v3.0
      •1•11•0•0•Updated May 10, 2023May 10, 2023

    • pangeblocks-experiments

      Public
      Experiments to evaluate graph constructions made with pangeblocks and other tools
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 4, 2023Apr 4, 2023

    • Wild-pBWT

      Public
      PBWT-based algorithm for identifying all Maximal Perfect Haplotype Blocks with Wildcards
      haplotypesbwthaplotype-blockspbwt
      C++
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Apr 3, 2023Apr 3, 2023

    • malva

      Public
      genotyping by Mapping-free ALternate-allele detection of known VAriants
      bioinformaticsngsvcfalignment-freegenotyping
      C
      •
      GNU General Public License v3.0
      •4•10•3•0•Updated Mar 6, 2023Mar 6, 2023

    • pygfa

      Public
      A library to manage GFA files
      Python
      •
      MIT License
      •3•7•3•0•Updated Mar 1, 2023Mar 1, 2023

    • cancer_ea

      Public
      cancer phylogeny genetic programming
      Python
      •2•2•0•0•Updated Feb 8, 2023Feb 8, 2023

    • deap

      Public
      Distributed Evolutionary Algorithms in Python
      Python
      •
      GNU Lesser General Public License v3.0
      •1.1k•1•0•0•Updated Feb 8, 2023Feb 8, 2023

    • MALVIRUS

      Public
      A fast and accurate tool for genotyping haploid individuals (such as SARS-CoV-2)
      kmeralignment-freevirologygenotyping-by-sequencinggenotypingsars-cov-2
      JavaScript
      •
      GNU General Public License v3.0
      •2•2•0•0•Updated Dec 13, 2022Dec 13, 2022

    • CouGaR-g

      Public
      Frequence Chaos Game Representation of DNA with Deep Learning
      Python
      •
      GNU General Public License v3.0
      •4•2•0•0•Updated Sep 25, 2022Sep 25, 2022

    • rs-vgaligner

      Public
      Rust implementation of ekg's dozyg
      bioinformaticsanchorsalignmentkmerpoachainingrust
      Rust
      •
      MIT License
      •0•9•0•0•Updated Jun 27, 2022Jun 27, 2022

    • Rearrangement-Distances

      Public
      Rearrangement Distances journal paper
      TeX
      •0•0•0•0•Updated Apr 19, 2022Apr 19, 2022

    • MALVIRUS-data

      Public
      Datasets accompanying MALVIRUS
      Python
      •0•0•0•0•Updated Mar 28, 2022Mar 28, 2022

    • persistent-phylogeny

      Public
      C++
      •
      MIT License
      •2•0•0•0•Updated Feb 22, 2022Feb 22, 2022

    • supervised-dna

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Feb 22, 2022Feb 22, 2022

    • kfinger

      Public
      A pipeline for computing overlaps between long reads based on theoretical properties of Lyndon factorizations.
      overlappacbiolyndon-factors
      Python
      •0•3•0•0•Updated Jan 31, 2022Jan 31, 2022

    • MALVIRUS-repro

      Public
      Reproducibility of MALVIRUS experiments
      C++
      •0•0•0•0•Updated Oct 8, 2021Oct 8, 2021

    • celluloid

      Public
      Celluloid: clustering single cell sequencing data around centroids
      Python
      •
      MIT License
      •1•0•0•0•Updated Jun 13, 2021Jun 13, 2021

    • shark

      Public
      Mapping-free software for fishing relevant reads in an RNA-Seq sample
      bioinformaticsrna-seqfilteringalignment-free
      C++
      •
      GNU General Public License v3.0
      •1•18•0•0•Updated Dec 9, 2020Dec 9, 2020