Alternatives and similar repositories for GFF3toolkit

Users that are interested in GFF3toolkit are comparing it to the libraries listed below

• cgat-developers / cgat-apps

  View on GitHub
  cgat-apps repository
  ☆34Apr 9, 2025Updated 10 months ago
• EI-CoreBioinformatics / mikado

  View on GitHub
  Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to s…
  ☆109Jan 30, 2026Updated 2 weeks ago
• OmarOakheart / nPhase

  View on GitHub
  Ploidy agnostic phasing pipeline and algorithm
  ☆49Jan 3, 2024Updated 2 years ago
• EVidenceModeler / EVidenceModeler

  View on GitHub
  source code for EVM
  ☆122Nov 29, 2024Updated last year
• reubwn / collinearity

  View on GitHub
  scripts to parse and analyse MCScanX collinearity output
  ☆32Mar 3, 2020Updated 5 years ago
• tanghaibao / allhic

  View on GitHub
  Genome scaffolding based on HiC data in heterozygous and high ploidy genomes
  ☆60Jan 3, 2025Updated last year
• Adamtaranto / TRF2GFF

  View on GitHub
  Convert Tandem Repeat Finder dat file output into gff3 format
  ☆30Nov 9, 2025Updated 3 months ago
• NBISweden / AGAT

  View on GitHub
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆556Jan 13, 2026Updated last month
• ablab / stringdecomposer

  View on GitHub
  Tool for decomposition centromeric assemblies and long reads into monomers
  ☆37Sep 17, 2022Updated 3 years ago
• SunPengChuan / wgdi

  View on GitHub
  WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes
  ☆159Nov 4, 2025Updated 3 months ago
• alekseyzimin / EviAnn_release

  View on GitHub
  This is the standalone version of the EviAnn pipeline
  ☆136Feb 5, 2026Updated last week
• agshumate / Liftoff

  View on GitHub
  An accurate GFF3/GTF lift over pipeline
  ☆526Aug 1, 2023Updated 2 years ago
• milkschen / leviosam2

  View on GitHub
  Fast and accurate coordinate conversion between assemblies
  ☆118Oct 9, 2025Updated 4 months ago
• phasegenomics / matlock

  View on GitHub
  Simple tools for working with Hi-C data
  ☆18Dec 19, 2018Updated 7 years ago
• tangerzhang / ALLHiC

  View on GitHub
  ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
  ☆177Oct 20, 2024Updated last year
• zhangrengang / TEsorter

  View on GitHub
  TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes
  ☆104Nov 17, 2025Updated 2 months ago
• gpertea / gffcompare

  View on GitHub
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆257Jul 12, 2025Updated 7 months ago
• Gaius-Augustus / BRAKER

  View on GitHub
  BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…
  ☆445Oct 20, 2025Updated 3 months ago
• Gaius-Augustus / Augustus

  View on GitHub
  Genome annotation with AUGUSTUS
  ☆327Aug 15, 2025Updated 5 months ago
• baoxingsong / AnchorWave

  View on GitHub
  Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation
  ☆184Oct 15, 2025Updated 3 months ago
• RacconC / gtftools

  View on GitHub
  ☆16May 7, 2023Updated 2 years ago
• qiao-xin / DupGen_finder

  View on GitHub
  A pipeline used to identify different modes of duplicated gene pairs
  ☆117Jul 22, 2025Updated 6 months ago
• yeeus / GCI

  View on GitHub
  A program for assessing the T2T genome continuity
  ☆92Dec 14, 2025Updated last month
• Atvar2 / plotHicGenome

  View on GitHub
  The tools are used for displaying hic signal of genome
  ☆24Jan 4, 2021Updated 5 years ago
• TickingClock1992 / RIdeogram

  View on GitHub
  ☆192Sep 22, 2020Updated 5 years ago
• usadellab / Helixer

  View on GitHub
  Using Deep Learning to predict gene annotations
  ☆275Feb 5, 2026Updated last week
• tacorna / taco

  View on GitHub
  Multi-sample transcriptome assembly from RNA-Seq
  ☆25Jun 10, 2018Updated 7 years ago
• Yandell-Lab / maker

  View on GitHub
  Genome Annotation Pipeline
  ☆43Aug 20, 2024Updated last year
• VIB-PSB / ksrates

  View on GitHub
  ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-orth…
  ☆20Jan 21, 2026Updated 3 weeks ago
• Markusjsommer / TD2

  View on GitHub
  TD2
  ☆31Jan 14, 2026Updated 3 weeks ago
• hillerlab / CESAR2.0

  View on GitHub
  ☆28Dec 1, 2022Updated 3 years ago
• bcgsc / ntSynt

  View on GitHub
  Detecting multi-genome synteny using minimizer graph mapping
  ☆101Updated this week
• Immortal2333 / Telomeres_and_Centromeres

  View on GitHub
  This is a method to find telomeres and centromeres in plants.
  ☆42Jun 17, 2023Updated 2 years ago
• tpoorten / dotPlotly

  View on GitHub
  Generate an interactive dot plot from mummer or minimap alignments
  ☆210Jan 17, 2024Updated 2 years ago
• dentearl / mafTools

  View on GitHub
  Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.
  ☆109Jun 17, 2022Updated 3 years ago
• bergmanlab / TELR

  View on GitHub
  TELR is a fast non-reference transposable element detector from long read sequencing data.
  ☆35Jul 27, 2023Updated 2 years ago
• tao-bioinfo / gff3sort

  View on GitHub
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆50Jun 27, 2020Updated 5 years ago
• shelkmike / Mabs

  View on GitHub
  Mabs, a genome assembly tool that optimizes parameters of Hifiasm and Flye
  ☆35Dec 24, 2025Updated last month
• Gaius-Augustus / GALBA

  View on GitHub
  GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the sc…
  ☆148Jan 27, 2025Updated last year