Alternatives and similar repositories for jcvi

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

• oushujun / EDTA

  View on GitHub
  Extensive de-novo TE Annotator
  ☆429Oct 12, 2025Updated 4 months ago
• wyp1125 / MCScanX

  View on GitHub
  MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
  ☆276Oct 4, 2025Updated 4 months ago
• tpoorten / dotPlotly

  View on GitHub
  Generate an interactive dot plot from mummer or minimap alignments
  ☆211Jan 17, 2024Updated 2 years ago
• schneebergerlab / syri

  View on GitHub
  Synteny and Rearrangement Identifier
  ☆447Apr 29, 2025Updated 9 months ago
• davidemms / OrthoFinder

  View on GitHub
  Phylogenetic orthology inference for comparative genomics
  ☆829Jul 15, 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…
  ☆446Oct 20, 2025Updated 3 months ago
• malonge / RagTag

  View on GitHub
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆554Feb 14, 2024Updated 2 years ago
• oushujun / LTR_retriever

  View on GitHub
  LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…
  ☆215Jun 25, 2025Updated 7 months ago
• tangerzhang / ALLHiC

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

  View on GitHub
  Official home of genome aligner based upon notion of Cactus graphs
  ☆652Updated this week
• schneebergerlab / plotsr

  View on GitHub
  Tool to plot synteny and structural rearrangements between genomes
  ☆341Apr 7, 2025Updated 10 months ago
• chhylp123 / hifiasm

  View on GitHub
  Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
  ☆742Mar 18, 2025Updated 10 months ago
• mummer4 / mummer

  View on GitHub
  Mummer alignment tool
  ☆548Feb 4, 2025Updated last year
• PASApipeline / PASApipeline

  View on GitHub
  PASA software
  ☆197Feb 12, 2025Updated last year
• qiao-xin / DupGen_finder

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

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

  View on GitHub
  k-mer based assembly evaluation
  ☆338Jun 28, 2024Updated last year
• zengxiaofei / HapHiC

  View on GitHub
  HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data
  ☆254Jan 5, 2026Updated last month
• pangenome / pggb

  View on GitHub
  the pangenome graph builder
  ☆478Dec 8, 2025Updated 2 months 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
• BGI-Qingdao / TGS-GapCloser

  View on GitHub
  A gap-closing software tool that uses long reads to enhance genome assembly.
  ☆231Sep 6, 2024Updated last year
• eggnogdb / eggnog-mapper

  View on GitHub
  Fast genome-wide functional annotation through orthology assignment
  ☆700Jun 18, 2025Updated 7 months ago
• NBISweden / AGAT

  View on GitHub
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆559Jan 13, 2026Updated last month
• mahulchak / quickmerge

  View on GitHub
  A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
  ☆207Nov 18, 2022Updated 3 years ago
• EVidenceModeler / EVidenceModeler

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

  View on GitHub
  Using Deep Learning to predict gene annotations
  ☆276Feb 5, 2026Updated last week
• baoxingsong / AnchorWave

  View on GitHub
  Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation
  ☆184Oct 15, 2025Updated 4 months ago
• hillerlab / TOGA

  View on GitHub
  TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annot…
  ☆203Nov 23, 2025Updated 2 months ago
• zhangrengang / TEsorter

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

  View on GitHub
  Fast genome analysis from unassembled short reads
  ☆311Apr 8, 2024Updated last year
• hahnlab / CAFE5

  View on GitHub
  Version 5 of the CAFE phylogenetics software
  ☆159Feb 12, 2025Updated last year
• KamilSJaron / smudgeplot

  View on GitHub
  Inference of ploidy and heterozygosity structure using whole genome sequencing data
  ☆291Updated this week
• aidenlab / 3d-dna

  View on GitHub
  3D de novo assembly (3D DNA) pipeline
  ☆222Nov 29, 2023Updated 2 years ago
• Nextomics / NextDenovo

  View on GitHub
  Fast and accurate de novo assembler for long reads
  ☆398May 10, 2024Updated last year
• nextgenusfs / funannotate

  View on GitHub
  Eukaryotic Genome Annotation Pipeline
  ☆380Jan 21, 2026Updated 3 weeks ago
• hewm2008 / NGenomeSyn

  View on GitHub
  Any Way to Show Multi genomic Synteny
  ☆218Jul 4, 2025Updated 7 months ago
• dfguan / purge_dups

  View on GitHub
  haplotypic duplication identification tool
  ☆275Oct 30, 2025Updated 3 months ago
• deeptools / pyGenomeTracks

  View on GitHub
  python module to plot beautiful and highly customizable genome browser tracks
  ☆864Jul 10, 2024Updated last year
• Nextomics / NextPolish

  View on GitHub
  Fast and accurately polish the genome generated by long reads.
  ☆240Jan 9, 2025Updated last year