PhyloSD: Phylogenomic Subgenome Detection pipeline
☆11Jun 24, 2022Updated 3 years ago
Alternatives and similar repositories for allopolyploids
Users that are interested in allopolyploids are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Perl script for manipulating multiple sequence alignments for phylogenetic reconstruction☆11Sep 29, 2014Updated 11 years ago
- Homologizer: phasing gene copies into polyploid subgenomes☆11Feb 3, 2026Updated last month
- This pipeline is used to distinguish allotetraploid subgenomes.☆11Apr 8, 2024Updated last year
- A set of scripts for the assembly of chloroplast genomes out of whole-genome sequencing reads☆12May 2, 2019Updated 6 years ago
- wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication☆37Feb 12, 2025Updated last year
- ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-orth…☆23Jan 21, 2026Updated 2 months ago
- Fast and frugal disk based k-mer counter☆14Apr 1, 2021Updated 4 years ago
- Scripts and resources for the haploblocks manuscript☆18Mar 20, 2020Updated 6 years ago
- ☆26Mar 23, 2024Updated 2 years ago
- a fork of the gap-closing pipeline PBJelly☆15Jan 7, 2019Updated 7 years ago
- Software GMATA for SSR mining, marker designing, genotyping, plot etc.☆17Oct 6, 2025Updated 5 months ago
- YAGCloser: Yet-Another-Gap-Closer based on spanning of long reads.☆12Nov 6, 2025Updated 4 months ago
- this project is content about my bioinformation analysis code .it may have R,Shell,Python.☆20Nov 9, 2023Updated 2 years ago
- Chromosome-level synteny plotting using orthologous regions☆32Sep 19, 2024Updated last year
- Generation of OrthoDB protein sets for gene prediction experiments☆11Aug 8, 2024Updated last year
- Python scripts to run tandem repeat finder program (Benson, 1999) and parse the results☆13Mar 11, 2019Updated 7 years ago
- Reduction of Althaps and Duplicate Contigs for Improved Hi-C Scaffolding☆20Mar 3, 2025Updated last year
- PAF (pairwise alignment format) validator based on extended CIGAR strings☆15Aug 10, 2025Updated 7 months ago
- ☆19Feb 15, 2025Updated last year
- ☆21Aug 8, 2024Updated last year
- Demographic analysis of Brassica oleracea☆10Jan 30, 2026Updated last month
- Efficient retrieval, download, and unification of genomic data from leading biodiversity databases☆18Mar 16, 2026Updated last week
- PECAT, a phased error correct and assembly tool☆59Dec 8, 2025Updated 3 months ago
- Code and Tutorials for Running the MArginal ePIstasis Test (MAPIT)☆19Nov 29, 2022Updated 3 years ago
- Phasing reads with secondary alignments☆22Nov 30, 2024Updated last year
- Pipeline to perform the allele-specific expression analysis (based on the work by Skelly et al. 2011)☆12May 22, 2025Updated 10 months ago
- genome basic statistics tool (e.g. n50, n10, ng50,...)☆15Mar 5, 2012Updated 14 years ago
- VCF Observer is a VCF file analysis, comparison, and visualization tool.☆18Jan 3, 2025Updated last year
- Evolutionary Bioinformatics Toolkit (EBT)☆12Jul 14, 2020Updated 5 years ago
- Code for the Brassica oleracea/rapa/napus genomic comparison☆16Apr 29, 2021Updated 4 years ago
- De novo tandem repeat calling from PacBio HiFi data☆19Dec 5, 2025Updated 3 months ago
- FastK based version of Merqury☆32Jan 19, 2026Updated 2 months ago
- A gap-closing software tool that uses long reads to enhance genome assembly.☆23Apr 25, 2024Updated last year
- A Julia package for handle genome graph in the GFA format.☆11Sep 2, 2022Updated 3 years ago
- Long read aligner for cyclic and acyclic pangenome graphs☆40Dec 20, 2023Updated 2 years ago
- Pan-genome Construction and Population Structure Variation Calling pipeline☆45Sep 13, 2024Updated last year
- ☆14Oct 29, 2024Updated last year
- Tandem Repeats Finder: a program to analyze DNA sequences☆22Jul 30, 2025Updated 7 months ago
- Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)☆373Feb 13, 2025Updated last year