Python package and CLI for whole-genome duplication related analyses. **This package is deprecated in favor of** https://github.com/heche-psb/wgd.
☆86Jan 6, 2026Updated 5 months ago
Alternatives and similar repositories for wgd
Users that are interested in wgd are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- This python script can be used to detect Whole-genome duplication (WGD) with the dS based method.☆26Feb 22, 2019Updated 7 years ago
- ☆22Sep 12, 2019Updated 6 years ago
- ☆45Oct 29, 2022Updated 3 years ago
- To phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.☆73Jun 4, 2026Updated last week
- Instruction and scripts for reconstructing ancestral genome from pairwise syntenic blocks using MLGO☆13Oct 30, 2018Updated 7 years 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 iDentification of Subgenomes☆10Jul 7, 2022Updated 3 years ago
- WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes☆166Nov 4, 2025Updated 7 months ago
- ☆22Aug 8, 2024Updated last year
- Reconstruction of ancestral genome maps☆16Mar 29, 2018Updated 8 years ago
- wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication☆41May 27, 2026Updated 2 weeks ago
- i-ADHoRe is a highly sensitive software tool to detect degenerated homology relations within and between different genomes.☆17Jun 28, 2024Updated last year
- LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…☆216May 12, 2026Updated last month
- Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.☆121Apr 7, 2021Updated 5 years ago
- ☆87Jul 12, 2024Updated last year
- 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.
- ☆29Jul 16, 2022Updated 3 years ago
- Robust identification of orthologous Synteny with the Orthology Index☆43Updated this week
- This pipeline is used to distinguish allotetraploid subgenomes.☆11Apr 8, 2024Updated 2 years ago
- Python library to facilitate genome assembly, annotation, and comparative genomics☆917May 2, 2026Updated last month
- A Python package for testing evolutionary hypotheses in genome-wide approaches.☆33Mar 5, 2021Updated 5 years ago
- GCE (genomic charactor estimator) is a bayes model based method to estimate the genome size, genomic repeat content and the heterozygsis…☆54Feb 27, 2020Updated 6 years ago
- RepeatIdentifier☆74Mar 19, 2025Updated last year
- Version 5 of the CAFE phylogenetics software☆171Mar 16, 2026Updated 3 months ago
- reference-free estimation of ploidy level from whole genome sequencing data based on de Bruijn graph☆18Jul 26, 2023Updated 2 years ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- A genome assembly assessment pipeline.☆38Jun 5, 2026Updated last week
- findGSE is a tool for estimating size of (heterozygous diploid or homozygous) genomes by fitting k-mer frequencies iteratively with a ske…☆38Jan 16, 2024Updated 2 years ago
- Homologizer: phasing gene copies into polyploid subgenomes☆13Feb 3, 2026Updated 4 months ago
- ☆78Dec 4, 2019Updated 6 years ago
- 3D de novo assembly (3D DNA) pipeline☆226Nov 29, 2023Updated 2 years ago
- Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation☆16Apr 29, 2025Updated last year
- TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes☆110Nov 17, 2025Updated 6 months ago
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆179Oct 20, 2024Updated last year
- haplotypic duplication identification tool☆287Oct 30, 2025Updated 7 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Simple tools for working with Hi-C data☆20Dec 19, 2018Updated 7 years ago
- A pipeline used to identify different modes of duplicated gene pairs☆120Jul 22, 2025Updated 10 months ago
- Synteny and Rearrangement Identifier☆473May 20, 2026Updated 3 weeks ago
- Inference of ploidy and heterozygosity structure using whole genome sequencing data☆296May 28, 2026Updated 2 weeks ago
- Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.☆29Mar 5, 2018Updated 8 years ago
- Extensive de-novo TE Annotator☆448May 12, 2026Updated last month
- source code for EVM☆124Nov 29, 2024Updated last year