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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy feedback >> testbranchdnds.bf script http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1334069211 Message started by ksenia on Apr 10^th, 2012 at 7:46am

Title: testbranchdnds.bf script
Post by ksenia on Apr 10^th, 2012 at 7:46am

Hello! I tried to run the script below
but "All Branches" is not suitable,
is there any command to select all branches at once?

inputRedirect = {};
inputRedirect["01"]="Universal";
inputRedirect["02"]="gene.nex";
inputRedirect["03"]="None";
inputRedirect["04"]="Default";
inputRedirect["05"]="Default";
inputRedirect["06"]="gene.nwk";
inputRedirect["07"]="All Branches";
inputRedirect["08"]="";
inputRedirect["09"]="1";
inputRedirect["10"]="";

I would appreciate any help! :)

Title: Re: testbranchdnds.bf script
Post by Sergei on Apr 10^th, 2012 at 2:38pm

Hi Ksenia,

For that particular analysis -- no (but it's a good idea to add such a feature). Incidentally, we have released a much better analysis for testing branch-level selective pressures (BranchSiteREL.bf) and I would encourage you to use it instead of testbranchdnds.bf. In BranchSiteREL, all branches are tested automatically.

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Title: Re: testbranchdnds.bf script
Post by ksenia on Apr 10^th, 2012 at 3:36pm

Sergei,

thank you a lot for information and advice!

Ksenia

Title: Re: testbranchdnds.bf script
Post by ksenia on Apr 11^th, 2012 at 9:57am

Hi!
I've got one more question: how to export analysis in bf file in command line without GUI?
Ksenia

Title: Re: testbranchdnds.bf script
Post by Sergei on Apr 11^th, 2012 at 10:00am

Hi Ksenia,

Sorry, not sure what you mean by "export analysis".

Sergei

Title: Re: testbranchdnds.bf script
Post by ksenia on Apr 11^th, 2012 at 10:15am

GUI gives an ability to save results in bf file

(HyPhy Console: Analyses->Results->Save Results->Export Analysis->bf file)

Ksenia

Title: Re: testbranchdnds.bf script
Post by Sergei on Apr 12^th, 2012 at 2:09pm

Hi Ksenia,

BranchSiteREL actually writes the analysis (.bf) file with as a part of its normal execution.

Sergei