Python library to facilitate genome assembly, annotation, and comparative genomics
☆918May 2, 2026Updated last month
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!☆289Oct 4, 2025Updated 8 months ago
- Extensive de-novo TE Annotator☆450May 12, 2026Updated last month
- Generate an interactive dot plot from mummer or minimap alignments☆219Jan 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…☆217May 12, 2026Updated last month
- Synteny and Rearrangement Identifier☆473May 20, 2026Updated 3 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.
- Phylogenetic orthology inference for comparative genomics☆858Jul 15, 2025Updated 11 months ago
- BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…☆463Apr 12, 2026Updated 2 months ago
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆179Oct 20, 2024Updated last year
- Tools for fast and flexible genome assembly scaffolding and improvement☆567Feb 14, 2024Updated 2 years ago
- PASA software☆200Feb 12, 2025Updated last year
- A pipeline used to identify different modes of duplicated gene pairs☆120Jul 22, 2025Updated 10 months ago
- Official home of genome aligner based upon notion of Cactus graphs☆687Updated this week
- Hifiasm: a haplotype-resolved assembler for accurate Hifi reads☆783May 31, 2026Updated 2 weeks ago
- Mummer alignment tool☆561Feb 4, 2025Updated last year
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Tool to plot synteny and structural rearrangements between genomes☆348Apr 7, 2025Updated last year
- k-mer based assembly evaluation☆343May 21, 2026Updated 3 weeks ago
- TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes☆110Nov 17, 2025Updated 7 months ago
- HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data☆271Jan 5, 2026Updated 5 months ago
- An accurate GFF3/GTF lift over pipeline☆545Aug 1, 2023Updated 2 years ago
- Any Way to Show Multi genomic Synteny☆229Jul 4, 2025Updated 11 months ago
- A gap-closing software tool that uses long reads to enhance genome assembly.☆240Sep 6, 2024Updated last year
- WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes☆166Nov 4, 2025Updated 7 months ago
- Using Deep Learning to predict gene annotations☆292May 21, 2026Updated 3 weeks ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Version 5 of the CAFE phylogenetics software☆171Mar 16, 2026Updated 3 months ago
- Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation☆194Oct 15, 2025Updated 8 months ago
- Identify and find telomeres, or telomeric repeats in a genome.☆165Nov 24, 2025Updated 6 months ago
- 3D de novo assembly (3D DNA) pipeline☆226Nov 29, 2023Updated 2 years ago
- Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/☆572May 18, 2026Updated last month
- the pangenome graph builder☆502Mar 31, 2026Updated 2 months ago
- Fast genome analysis from unassembled short reads☆323Apr 8, 2024Updated 2 years ago
- Fast genome-wide functional annotation through orthology assignment☆745May 22, 2026Updated 3 weeks ago
- TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annot…☆207Nov 23, 2025Updated 6 months ago
- 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.
- Inference of ploidy and heterozygosity structure using whole genome sequencing data☆296May 28, 2026Updated 3 weeks ago
- A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.☆211Nov 18, 2022Updated 3 years ago
- haplotypic duplication identification tool☆287Oct 30, 2025Updated 7 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 5 months ago
- source code for EVM☆124Nov 29, 2024Updated last year
- SynVisio is an interactive multiscale visualization tool that lets you explore the results of McScanX a popular synteny and collinearity …☆94May 30, 2026Updated 2 weeks ago
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆440Mar 28, 2024Updated 2 years ago