Python library to facilitate genome assembly, annotation, and comparative genomics
☆929Sep 14, 2026Updated this week
Alternatives and similar repositories for jcvi
Users that are interested in jcvi are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!☆298Oct 4, 2025Updated 11 months ago
- Extensive de-novo TE Annotator☆470Sep 10, 2026Updated last week
- Generate an interactive dot plot from mummer or minimap alignments☆220Jan 17, 2024Updated 2 years ago
- LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…☆220Jun 30, 2026Updated 2 months ago
- Synteny and Rearrangement Identifier☆489Jul 1, 2026Updated 2 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Phylogenetic orthology inference for comparative genomics☆872Jul 15, 2025Updated last year
- BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…☆467Jun 17, 2026Updated 3 months ago
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆180Oct 20, 2024Updated last year
- Tools for fast and flexible genome assembly scaffolding and improvement☆575Feb 14, 2024Updated 2 years ago
- A pipeline used to identify different modes of duplicated gene pairs☆123Jul 22, 2025Updated last year
- PASA software☆204Feb 12, 2025Updated last year
- Official home of genome aligner based upon notion of Cactus graphs☆707Updated this week
- Hifiasm: a haplotype-resolved assembler for accurate Hifi reads☆813May 31, 2026Updated 3 months ago
- Mummer alignment tool☆575Feb 4, 2025Updated last year
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Tool to plot synteny and structural rearrangements between genomes☆355Jul 27, 2026Updated last month
- k-mer based assembly evaluation☆355Jul 6, 2026Updated 2 months ago
- HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data☆283Aug 10, 2026Updated last month
- Using Deep Learning to predict gene annotations☆305Jul 22, 2026Updated last month
- An accurate GFF3/GTF lift over pipeline☆557Aug 1, 2023Updated 3 years ago
- Identify and find telomeres, or telomeric repeats in a genome.☆176Nov 24, 2025Updated 9 months ago
- TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes☆113Nov 17, 2025Updated 10 months ago
- Any Way to Show Multi genomic Synteny☆230Jul 4, 2025Updated last year
- WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes☆174Nov 4, 2025Updated 10 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- A gap-closing software tool that uses long reads to enhance genome assembly.☆249Sep 6, 2024Updated 2 years ago
- Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation☆203Aug 17, 2026Updated last month
- Version 5 of the CAFE phylogenetics software☆178Mar 16, 2026Updated 6 months ago
- Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/☆588Sep 7, 2026Updated last week
- 3D de novo assembly (3D DNA) pipeline☆229Nov 29, 2023Updated 2 years ago
- the pangenome graph builder☆515Jul 24, 2026Updated last month
- Fast genome analysis from unassembled short reads☆326Apr 8, 2024Updated 2 years ago
- Fast genome-wide functional annotation through orthology assignment☆780Aug 13, 2026Updated last month
- Inference of ploidy and heterozygosity structure using whole genome sequencing data☆301Sep 3, 2026Updated 2 weeks ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- haplotypic duplication identification tool☆295Oct 30, 2025Updated 10 months ago
- Python package and CLI for whole-genome duplication related analyses. **This package is deprecated in favor of** https://github.com/heche…☆86Jan 6, 2026Updated 8 months ago
- A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.☆213Nov 18, 2022Updated 3 years ago
- TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annot…☆211Nov 23, 2025Updated 9 months ago
- source code for EVM☆128Nov 29, 2024Updated last year
- Neural network classification of TE☆102Apr 3, 2026Updated 5 months ago
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆444Mar 28, 2024Updated 2 years ago