legumeinfo / pandagmaView external linksLinks
Generate pan-gene sets, given a collection of genome assemblies and corresponding gene models.
☆20Feb 10, 2026Updated last week
Alternatives and similar repositories for pandagma
Users that are interested in pandagma are comparing it to the libraries listed below
Sorting:
- PanEffect is a JavaScript framework to explore variant effects across a pangenome. The tool has two views that allows a user to (1) expl…☆13Jan 30, 2024Updated 2 years ago
- Resistify is a program which rapidly identifies and classifies plant resistance genes from protein sequences. It is designed to be lightw…☆41Feb 9, 2026Updated last week
- Scripting analyses of genomes in Ensembl Plants☆42Jan 1, 2026Updated last month
- scripts for the project of seven thaliana genomes assembly☆42May 22, 2021Updated 4 years ago
- a precise pangenome browser combining linear and graph-based pan-genome☆13Jul 16, 2024Updated last year
- ☆13Nov 15, 2017Updated 8 years ago
- Genotyping lots of samples with big pangenomes☆11Oct 30, 2025Updated 3 months ago
- lace up GFA files using panSN path name sub-ranges to coordinate the lacing☆14Jul 30, 2025Updated 6 months ago
- TQSLE v1.0 released☆10Aug 29, 2023Updated 2 years ago
- SINE annotation tool for plant genomes☆18Jan 21, 2024Updated 2 years ago
- COsine SImilarity-based Genotyper using pangenomes☆25Jan 23, 2026Updated 3 weeks ago
- This repository contains relevant code and explanation for ”Leveraging a phased pangenome to design ideal haplotypes for hybrid potato br…☆34Oct 29, 2025Updated 3 months ago
- A web-based, interactive pangenome visualization tool☆21Apr 10, 2023Updated 2 years ago
- Identification of conserved non-coding sequences in plants☆32Feb 4, 2026Updated last week
- Create a pseudohaploid assembly from a partially resolved diploid assembly☆32Nov 22, 2019Updated 6 years ago
- Some components that speed up and reduce resource cost for original ALLHiC☆14Jun 21, 2025Updated 7 months ago
- FastK based version of Merqury☆32Jan 19, 2026Updated 3 weeks ago
- An R package for comparative transcriptomic analyses of hybrids and their progenitors☆15Sep 5, 2024Updated last year
- A viewer for multiple alignment format (MAF) files in JBrowse 2☆14Jan 31, 2026Updated 2 weeks ago
- Synteny matrix representation with maximum likelihood pipeline☆16Jul 7, 2021Updated 4 years ago
- Constructing a pangenome gene graph☆204Aug 11, 2025Updated 6 months ago
- ☆16Mar 17, 2023Updated 2 years ago
- A tool for quick and accurate calculation of syntenic diversity.☆42Sep 22, 2025Updated 4 months ago
- A rapid and accurate ensemble pipeline for graph-based variant genotyping with lower depth of short reads☆49Sep 22, 2025Updated 4 months ago
- Bash scripts and data used in pantranscriptomic paper☆24Oct 21, 2022Updated 3 years ago
- An R package to infer and analyze synteny networks from protein sequences☆36Jul 23, 2025Updated 6 months ago
- NLR-Annotator upload☆76Jul 19, 2023Updated 2 years ago
- Copy number variant caller and depth visualization utility for PacBio HiFi reads☆47Oct 22, 2024Updated last year
- Rust package for constructing and analyzing phylogenies. (unpolished & unmaintained)☆15May 1, 2025Updated 9 months ago
- PAF (pairwise alignment format) validator based on extended CIGAR strings☆15Aug 10, 2025Updated 6 months ago
- ☆14Jul 27, 2019Updated 6 years ago
- The IntroBlocker ancestry inference algorithm☆17Oct 24, 2023Updated 2 years ago
- ☆44May 8, 2024Updated last year
- Genetic maps in autopolyploids☆31Jan 12, 2026Updated last month
- BITACORA: A Bioinformatics tool for gene family annotation☆53Dec 10, 2025Updated 2 months ago
- Mumemto: multi-MUM and MEM finding across pangenomes☆128Dec 8, 2025Updated 2 months ago
- ☆18Jan 29, 2025Updated last year
- ☆21Dec 13, 2024Updated last year
- Python library to identify Identical By State regions☆22Mar 19, 2023Updated 2 years ago