https://github.com/applicativesystem/pangenome-single-copy-gene

single copy pangenome analysis from alignments to phylogenomics
https://github.com/applicativesystem/pangenome-single-copy-gene

bioinformatics bioinformatics-analysis genome-analysis genome-analysis-annotation genome-pangenome pangenome pangenome-pipeline

Last synced: 18 days ago
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single copy pangenome analysis from alignments to phylogenomics

• Host: GitHub
• URL: https://github.com/applicativesystem/pangenome-single-copy-gene
• Owner: applicativesystem
• License: mit
• Created: 2024-08-19T19:00:00.000Z (5 months ago)
• Default Branch: main
• Last Pushed: 2024-09-12T08:23:10.000Z (4 months ago)
• Last Synced: 2024-11-10T20:18:15.689Z (about 2 months ago)
• Topics: bioinformatics, bioinformatics-analysis, genome-analysis, genome-analysis-annotation, genome-pangenome, pangenome, pangenome-pipeline
• Language: Shell
• Homepage:
• Size: 2.93 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# pangenome-single-copy-gene

- a single copy gene analysis pangenome which allows for the orthology already computed and allows for the alignment and phylogeny building using three alignment approaches and also allows for the GTRCAT and GTRGAMA model with 1000 bootstrap.

- To check the file conversion it iterates the first files at the start and see if the number matches to the number of the genes present in each files. If the number doesnt matches then it will exit such as

> Updated 2024-2-17

added the support for all options and selected options and also added support for the multi-tool phylogeny. 

Gaurav Sablok \

University of Potsdam,\

Potsdam,Germany