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Old 10-31-2013, 11:55 AM   #2
jflowers002
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Location: Seattle

Join Date: Jan 2013
Posts: 6
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Well, I will answer my own question. One inherent issue that i believe caused this trouble was my blast parameters. I had 100 genomes and I only allowed 250 hits since I was concerned about diskspace and time. Orhtomcl acutally recommends not limiting this (https://docs.google.com/document/d/1...xqDAMjyP_w/pub).

I figured that 2.5 orthologs in each genome for the same gene was enough, but maybe not. I am currently rerunning the process with a larger allowed hits and hopefully this will fix it.
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