Orthomclpairs Problems -----Orthomcl

Question

[wang.qiang.prc]

When I use orthomclPairs, it produced three files. However, all of these three files ( coothologs.txt, inparalogs.txt and orthologs.txt ) are empty..

Anyone can give me suggestions?? Thanks

[arnstrm]

Give us some more details: what command did you run? Did it generate mclinput file? how many genomes are you using for orthoMCL?

Answer 1

[Peter vH]

When you do the blast search, do you do all vs all blast (i.e. not just blast of query set vs a different set)? If you don't, you get these three zero length files.