OrthoFinder: Diamond or Blast? Which is better?
I saw some research showed that blast is 15% more sensitive than diamond, while I am interested in using blastp in OrthoFinder, I can't seemed to find the parameter of Blast being documented, there is also nothing in the log.file from Orthofinder output. How did blastp from Orthofinder select an ortholog? based on which parameter cutoff? I believe using OrthoFinder is better than bidirectional blast in finding orthologs, but I hope I can find more documentation that support this thought. The only input parameter Orthofinder accepted is -S for selecting propgram of interest( is there any other blast option ? ) . Any advice, suggestion, post that I have missed from biostar or criticism are welcome. Thank you in advance.
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