A toolkit for prokaryotic comparative genomics
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Updated
Jun 3, 2024 - Python
A toolkit for prokaryotic comparative genomics
Pangenome-Analysis.py is written for extraction of core, accessory and unique genomes (Gene families and proteins) along with filtration of single copy orthologues, creation of binary and count matrices as well as removal of duplicates.
single copy pangenome analysis from alignments to phylogeny and support GTRCAT and GTRGAMA model
analyzing the pangenomes from the core genesets, estimates, the core genes, pangenomes, breakage in the phylogeny and also phylogenomics analysis.
The lumpy skin disease virus (LSDV) pangenome variation graph (PVG)
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