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testbranchdnds.bf script (Read 4254 times)

ksenia

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Curious HyPhy user

Posts: 5

testbranchdnds.bf script
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!

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Sergei

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Datamonkeys are forever...

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Re: testbranchdnds.bf script
Reply #1 - 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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ksenia YaBB Newbies Offline Curious HyPhy user Posts: 5	Re: testbranchdnds.bf script Reply #2 - Apr 10^th, 2012 at 3:36pm Sergei, thank you a lot for information and advice! Ksenia
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ksenia YaBB Newbies Offline Curious HyPhy user Posts: 5	Re: testbranchdnds.bf script Reply #3 - 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
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: testbranchdnds.bf script Reply #4 - Apr 11^th, 2012 at 10:00am Hi Ksenia, Sorry, not sure what you mean by "export analysis". Sergei
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ksenia YaBB Newbies Offline Curious HyPhy user Posts: 5	Re: testbranchdnds.bf script Reply #5 - 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
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: testbranchdnds.bf script Reply #6 - 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
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