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    12 repositories

    • SYNY

      Public
      The SYNY pipeline investigates synteny between species by reconstructing protein clusters from gene pairs.
      Perl
      •
      MIT License
      •4•38•0•0•Updated Nov 28, 2024Nov 28, 2024

    • A2GB

      Public
      A2GB is a pipeline that will transform the genome annotation files exported from Apollo in preparation for sequence submission to NCBI’s GenBank.
      genome-annotationevidence-basedfunction-prediction
      Perl
      •
      MIT License
      •0•3•0•0•Updated Jun 4, 2024Jun 4, 2024

    • MMH

      Public
      A simple pipeline to create and search HMM models against reference protein databases.
      hmmannotationhomology-search
      Perl
      •
      MIT License
      •1•0•0•0•Updated Jun 4, 2024Jun 4, 2024

    • Publication_scripts

      Public
      This repository contains scripts from published or submitted manuscripts.
      publication-datapublication-repositorypublication-code
      Perl
      •
      MIT License
      •3•3•0•0•Updated Jun 2, 2024Jun 2, 2024

    • Misc

      Public
      Miscellaneous scripts
      Perl
      •
      MIT License
      •0•0•0•0•Updated Jun 2, 2024Jun 2, 2024

    • ID16S

      Public
      This pipeline reconstructs the composition of species from 16S amplicon sequencing datasets.
      16samplicon-sequencingamplicon-sequence-analysis
      Perl
      •
      MIT License
      •0•1•0•0•Updated Jun 1, 2024Jun 1, 2024

    • SSRG

      Public
      The SSRG pipeline was created as a simple and focused tool to investigate genetic diversity between genomes.
      snpsgenetic-distance-estimationsfastq-datasets
      Perl
      •
      MIT License
      •4•4•0•0•Updated May 28, 2024May 28, 2024

    • 3DFI

      Public
      The 3DFI pipeline predicts the 3D structure of proteins and searches for structural homology in the 3D space.
      3d-structurepdb-filesstructural-homologs
      Perl
      •
      MIT License
      •7•19•0•0•Updated Mar 6, 2024Mar 6, 2024

    • A2A

      Public
      The A2A pipeline guides users from genome assembly to annotations.
      genome-annotation
      Python
      •1•1•0•0•Updated Jun 24, 2023Jun 24, 2023

    • QueGO

      Public
      The QueGO pipeline identifies potential homologs to proteins related to specific functionality.
      Perl
      •
      MIT License
      •0•1•0•0•Updated Dec 3, 2022Dec 3, 2022

    • alphafold

      Public
      Fork from AlphaFold to ensure compatibility with 3DFI
      Python
      •
      Apache License 2.0
      •2.3k•0•0•0•Updated Jul 1, 2022Jul 1, 2022

    • Old

      Public
      Contains old miscellaneous scripts for genomics. No longer maintained.
      deprecatedoldmiscellaneous
      Perl
      •
      MIT License
      •0•1•0•0•Updated Nov 27, 2020Nov 27, 2020