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@Gene-loss Gene loss

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    34 repositories

    • datasets

      Public
      NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.
      Jupyter Notebook
      •
      Other
      •45•0•0•0•Updated Dec 4, 2024Dec 4, 2024

    • DNA-editing

      Public
      DNA editing of retroelements
      Perl
      •
      MIT License
      •1•0•0•0•Updated Aug 28, 2024Aug 28, 2024

    • purge_dups

      Public
      haplotypic duplication identification tool
      C
      •
      MIT License
      •23•0•0•0•Updated Dec 23, 2023Dec 23, 2023

    • hh-suite

      Public
      Remote protein homology detection suite.
      C
      •
      GNU General Public License v3.0
      •136•0•0•0•Updated Sep 19, 2022Sep 19, 2022

    • Social_Spider_Evolutionary_Genomics

      Public
      R
      •1•0•0•0•Updated Jun 15, 2022Jun 15, 2022

    • TOGA

      Public
      TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.
      Python
      •
      MIT License
      •22•0•0•0•Updated May 9, 2022May 9, 2022

    • FalseDuplication

      Public
      false duplication and false gene gain research for VGP assemblies.
      Python
      •3•0•0•0•Updated May 2, 2022May 2, 2022

    • C9

      Public
      HTML
      •1•1•0•0•Updated Apr 25, 2022Apr 25, 2022

    • spaln

      Public
      Genome mapping and spliced alignment of cDNA or amino acid sequences
      C++
      •
      GNU General Public License v2.0
      •16•0•0•0•Updated Apr 14, 2022Apr 14, 2022

    • minimap2

      Public
      A versatile pairwise aligner for genomic and spliced nucleotide sequences
      C
      •
      Other
      •423•0•0•0•Updated Feb 14, 2022Feb 14, 2022

    • Bioinformatics-Training

      Public
      Bioinformatics training resources
      R
      •132•0•0•0•Updated Feb 2, 2022Feb 2, 2022

    • hyphy-analyses

      Public
      HyPhy standalone analyses
      PostScript
      •
      MIT License
      •17•0•0•0•Updated Jan 10, 2022Jan 10, 2022

    • COA1_GENE

      Public
      PostScript
      •1•1•0•0•Updated Dec 29, 2021Dec 29, 2021

    • JustOrthologs

      Public
      Python
      •16•0•0•0•Updated Nov 4, 2021Nov 4, 2021

    • enaBrowserTools

      Public
      A collection of scripts to assist in the retrieval of data from the ENA Browser
      Python
      •
      Apache License 2.0
      •15•1•0•0•Updated Oct 28, 2021Oct 28, 2021

    • A3-Evolution

      Public
      Resources supporting comparative and phylogenetic analysis of APOBEC3 genes
      Python
      •2•0•0•0•Updated Oct 18, 2021Oct 18, 2021

    • hcoErosions

      Public
      Python
      •
      MIT License
      •4•0•0•0•Updated Oct 14, 2021Oct 14, 2021

    • startstop

      Public
      R package for locating start and stop codons
      R
      •
      Other
      •1•0•0•0•Updated Oct 13, 2021Oct 13, 2021

    • FishLifeExonHarvesting

      Public
      Scripts for mining exons from genomes or transcriptomes. See Hughes et al. 2018 in PNAS for marker details.
      Python
      •1•0•0•0•Updated Jun 9, 2021Jun 9, 2021

    • RMRB

      Public
      This is an archive version of old RepBase library (v20170127) for RepeatMasker.
      18•0•0•0•Updated May 2, 2021May 2, 2021

    • Newick-validator

      Public
      Newick format validator, project for the Bioinformatic course, Università di Milano Bicocca
      Python
      •
      Apache License 2.0
      •4•0•0•0•Updated Apr 20, 2021Apr 20, 2021

    • alibaseq

      Public
      Alignment-Based Sequence extraction
      Python
      •
      MIT License
      •5•0•0•0•Updated Apr 1, 2021Apr 1, 2021

    • inquilineGenomics

      Public
      Inquiline comparative genomics project
      Shell
      •
      GNU General Public License v3.0
      •4•0•0•0•Updated Mar 16, 2021Mar 16, 2021

    • IGV-snapshot-automator

      Public
      Script to automatically create and run IGV snapshot batchscripts
      Python
      •
      GNU General Public License v3.0
      •50•0•0•0•Updated Nov 12, 2020Nov 12, 2020

    • blast-QC

      Public
      A Quality Control filter and parser for NCBI BLAST XML results.
      C
      •
      MIT License
      •4•0•0•0•Updated Aug 21, 2020Aug 21, 2020

    • PLGRKT

      Public
      Evidence for the loss of plasminogen receptor KT gene in the chicken
      Rich Text Format
      •2•0•0•0•Updated Aug 7, 2020Aug 7, 2020

    • gff3sort

      Public
      GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
      Perl
      •
      GNU General Public License v3.0
      •19•0•0•0•Updated Jun 27, 2020Jun 27, 2020

    • OMTools

      Public
      A software package for optical mapping data processing, analysis and visualization
      Java
      •4•0•0•0•Updated Jun 19, 2020Jun 19, 2020

    • EDirectCookbook

      Public
      MIT License
      •54•0•0•0•Updated Jun 8, 2020Jun 8, 2020

    • OMBlast

      Public
      An alignment tool for optical mapping data
      Java
      •3•0•0•0•Updated May 29, 2020May 29, 2020