Suggestions for better and accurate tool for PanGenome analysis.
I am doing pan genome analysis of multiple genera. I am searching a tool which will work on protein files (I have annotated proteins for each genome). I wanted to run Roary, but it requires .gff files as well.
Any suggestions are welcomed.
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Dattatray Mongad
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Something like CD-HIT and then parse the output? probably it would works as first insigth to what you want to do, however I think this is a complicated job even for closely-related species, so, for multiple genera... please tell me if you find another suitable solution.
OrthoMCL/PorthoMCL/JustOrthologs.
(Fair warning, OrthoMCL is an absolute pain in the ass to use)
What organism is it?
I have several microbial genomes and protein files from multiple genera. I have tried BPGA but it cantbe automated.
Roary is the best tool to use. It will accept gbk inputs (or at least it certainly used to)
You could reannotate with prokka to get a gff if you really needed to.