How To Identify Paralogs In Orlomcl Clusters?
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It seems it is not straight forward to find out difference between the isoforms or in your case paralogs until there is reference genome arranged in chromosomes or at least in long scaffolds. If we have those long sequences, then you can map the sequences in a cluster using tools like protein2genome, est2genome and check if all of them are coming from relatively same coordinates (isoforms) or different co-ordinates (paralogs).