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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy feedback >> a summary or key to the batch files? http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1158096958 Message started by tlefebure on Sep 12^th, 2006 at 2:35pm

Title: a summary or key to the batch files?
Post by tlefebure on Sep 12^th, 2006 at 2:35pm

Hello,

I'm quite lost with the bunch of batch file that comes with HyPhy. Is there somewhere a description or summary of who is doing what?
For example, regarding positive selection, which one is doing SLAC, FEL, REL analyzes?
Also, when a method is described in a paper (e.g. MBE 2005 22(12):2375-85), can we identify which batch file is currently implementing it?

Thanks,
Tristan

Title: Re: a summary or key to the batch files?
Post by artpoon on Sep 12^th, 2006 at 3:26pm

Dear Tristan,

I agree that an indexing of the batch files would be very useful. Hopefully we'll get around to assembling one soon, in which we can associate literature citations with batch files. (And in my experience, our group's been pretty good about completing requested features.) For SLAC, FEL, and REL analyses, you probably want to have a look at the batch file QuickSelectionDetection.bf. :)

Best wishes,
- Art.