I am trying to cluster orthologs (and paralogs) at the protein level. I seem to be getting groups that have very disparate proteins, because they are of very different lengths and their alignments returned by MAFFT are extremely gappy. So I am considering playing around with the Inflation factor of MCL.
Some info about that is at http://micans.org/mcl/man/mcl.html. "A good set of starting values is 1.4, 2, 4, and 6." While I understand, in theory, the effect changing inflation factor will have on the coarseness of clustering, how can I practically determine the best inflation factor for my dataset if I do not have any extensive information on it a priori? Any thoughts? Thank you!