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A couple of tools I find indispensable for post orthomcl down-stream analysis.
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.
Scripts for comparative genomic analysis at the genome architechture and gene content level
We are taking existing orthoMcl Software Written Perl and Translating it to Python