Phylogenetic iDentification of Subgenomes
☆10Jul 7, 2022Updated 3 years ago
Alternatives and similar repositories for PhyDS
Users that are interested in PhyDS are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- These are scripts that I use frequently in genome annotation projects. Some of them have evolved awkwardly so the code is difficult to fo…☆16Nov 20, 2017Updated 8 years ago
- The code used in the manuscript titled "Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants".☆29Mar 19, 2021Updated 5 years ago
- This python script can be used to detect Whole-genome duplication (WGD) with the dS based method.☆26Feb 22, 2019Updated 7 years ago
- Main scripts and commands used to analyze goat population genetic and domestication☆19Mar 25, 2019Updated 7 years 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 2 months ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- R and Python scripts used to simulate gene trees under coalescent model and detect gene flow using triple frequency☆15Dec 15, 2022Updated 3 years ago
- Making diploid assembly becomes common practice for genomic study☆30Oct 2, 2017Updated 8 years ago
- From the comparison of two extant genomes and corresponding gene families, PhylDiag detects conserved segments, i.e. segments of chromoso…☆15Aug 7, 2023Updated 2 years ago
- ☆26Jan 26, 2026Updated 2 months ago
- A couple of tools I find indispensable for post orthomcl down-stream analysis.☆11Oct 2, 2019Updated 6 years ago
- ☆31Apr 7, 2025Updated 11 months ago
- Scripts and procedures for detecting positively selected genes and codons in primates☆22Nov 14, 2020Updated 5 years ago
- ☆15Nov 11, 2019Updated 6 years ago
- A pipeline used to identify different modes of duplicated gene pairs☆119Jul 22, 2025Updated 8 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click and start building anything your business needs.
- ☆21Aug 8, 2024Updated last year
- A powerful Perl module for simulating the genome digestions by restriction enzymes☆14Sep 10, 2024Updated last year
- Methylatino phasing using PacBio CCS reads☆14Dec 13, 2024Updated last year
- ABLE - Approximate Blockwise Likelihood Estimation☆17Jul 4, 2018Updated 7 years ago
- This is code for running Orthofinder -> PAML☆12Jul 27, 2016Updated 9 years ago
- ☆21Sep 14, 2022Updated 3 years ago
- B73Ab10 genome assembly methods☆16Jan 21, 2022Updated 4 years ago
- Tool set for processing fasta/fastq/table formated data. Usually they are perl scripts.☆56Mar 6, 2026Updated 2 weeks ago
- ☆76Apr 23, 2020Updated 5 years ago
- NordVPN Special Discount Offer • AdSave on top-rated NordVPN 1 or 2-year plans with secure browsing, privacy protection, and support for for all major platforms.
- Instruction and scripts for reconstructing ancestral genome from pairwise syntenic blocks using MLGO☆13Oct 30, 2018Updated 7 years ago
- Reconstruction of ancestral genome maps☆16Mar 29, 2018Updated 7 years ago
- To phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.☆70Mar 23, 2025Updated last year
- DFOIL: Introgression Testing for Five Taxa☆33May 15, 2021Updated 4 years ago
- Codes for Vmap1.1 and Vmap3☆11Jan 5, 2026Updated 2 months ago
- Taxon-aware analysis of clustered protein sequences☆31Jul 1, 2024Updated last year
- Tutorials on evolutionary genomics☆46Mar 11, 2022Updated 4 years ago
- Segmental duplication detection tool☆16Feb 7, 2023Updated 3 years ago
- scripts and intermediate files used to annotate TEs in Jiao et al.☆34Apr 12, 2018Updated 7 years ago
- DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- De novo lncRNA discovery pipeline, re-write of PLAR in shell and awk☆10Aug 2, 2023Updated 2 years ago
- ☆14Jul 13, 2020Updated 5 years ago
- ☆13Jan 20, 2026Updated 2 months ago
- A tool to infer species tree and phylogenetic network from multilocus data☆32Jul 2, 2020Updated 5 years ago
- Utilities and distributions for (birth-death) skyline models.☆10Aug 27, 2019Updated 6 years ago
- Script to help assessing the evolutionary history of a TE family☆16Sep 5, 2019Updated 6 years ago
- A box of genomics tools☆22Aug 26, 2020Updated 5 years ago