Python library to facilitate genome assembly, annotation, and comparative genomics
☆899Apr 2, 2026Updated 2 weeks ago
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!☆282Oct 4, 2025Updated 6 months ago
- Extensive de-novo TE Annotator☆439Apr 5, 2026Updated 2 weeks ago
- Generate an interactive dot plot from mummer or minimap alignments☆213Jan 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…☆214Mar 9, 2026Updated last month
- Synteny and Rearrangement Identifier☆462Mar 17, 2026Updated last month
- Wordpress hosting with auto-scaling - Free Trial • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Phylogenetic orthology inference for comparative genomics☆849Jul 15, 2025Updated 9 months ago
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆179Oct 20, 2024Updated 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…☆456Apr 12, 2026Updated last week
- Tools for fast and flexible genome assembly scaffolding and improvement☆563Feb 14, 2024Updated 2 years ago
- PASA software☆199Feb 12, 2025Updated last year
- A pipeline used to identify different modes of duplicated gene pairs☆119Jul 22, 2025Updated 8 months ago
- Official home of genome aligner based upon notion of Cactus graphs☆671Apr 3, 2026Updated 2 weeks ago
- Hifiasm: a haplotype-resolved assembler for accurate Hifi reads☆766Updated this week
- Mummer alignment tool☆554Feb 4, 2025Updated last year
- Serverless GPU API endpoints on Runpod - Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Tool to plot synteny and structural rearrangements between genomes☆344Apr 7, 2025Updated last year
- k-mer based assembly evaluation☆340Jun 28, 2024Updated last year
- TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes☆108Nov 17, 2025Updated 5 months ago
- Any Way to Show Multi genomic Synteny☆225Jul 4, 2025Updated 9 months ago
- An accurate GFF3/GTF lift over pipeline☆534Aug 1, 2023Updated 2 years ago
- HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data☆261Jan 5, 2026Updated 3 months ago
- A gap-closing software tool that uses long reads to enhance genome assembly.☆234Sep 6, 2024Updated last year
- Using Deep Learning to predict gene annotations☆283Mar 6, 2026Updated last month
- WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes☆163Nov 4, 2025Updated 5 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Version 5 of the CAFE phylogenetics software☆165Mar 16, 2026Updated last month
- Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation☆189Oct 15, 2025Updated 6 months ago
- Identify and find telomeres, or telomeric repeats in a genome.☆163Nov 24, 2025Updated 4 months ago
- 3D de novo assembly (3D DNA) pipeline☆223Nov 29, 2023Updated 2 years ago
- Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/☆569Apr 13, 2026Updated last week
- the pangenome graph builder☆491Mar 31, 2026Updated 2 weeks ago
- Fast genome-wide functional annotation through orthology assignment☆722Mar 24, 2026Updated 3 weeks ago
- Fast genome analysis from unassembled short reads☆318Apr 8, 2024Updated 2 years ago
- TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annot…☆205Nov 23, 2025Updated 4 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Inference of ploidy and heterozygosity structure using whole genome sequencing data☆293Feb 25, 2026Updated last month
- A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.☆210Nov 18, 2022Updated 3 years ago
- haplotypic duplication identification tool☆280Oct 30, 2025Updated 5 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 3 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 …☆94Nov 24, 2025Updated 4 months ago
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆434Mar 28, 2024Updated 2 years ago