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HYPHY Package >> HyPhy feedback >> How to mention the name of the nucleotide evolutionary model http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1352125819 Message started by RTuteja on Nov 5th, 2012 at 6:30am |
Title: How to mention the name of the nucleotide evolutionary model Post by RTuteja on Nov 5th, 2012 at 6:30am
Hi All,
Modelgenerator program has predicted that the best model for my sequences is TVM+I+G. I don't see this model in the menu while using singlebreakpointReco. Can you please suggest me the way to specify this model. I don't know what is the six letter designation for the models. Please help! Thanks, Reetu |
Title: Re: How to mention the name of the nucleotide evolutionary model Post by Sergei on Nov 5th, 2012 at 1:36pm |
Title: Re: How to mention the name of the nucleotide evolutionary model Post by RTuteja on Nov 12th, 2012 at 3:07am
Hi Seregi,
Thanks for your help so far on this. I could not find why I have to specify TVM == REV, instead of only TVM (are these submodels?). I have around 200 gene families for analysis. I am reading up in the area of nucl evolutionary models but any suggestions/hints from you will be a helpful to explore myself further. Many thanks for your help! Regards, Reetu |
Title: Re: How to mention the name of the nucleotide evolutionary model Post by RTuteja on Nov 16th, 2012 at 10:01am
Hi Sergei,
I am getting the following error while running Singlebreakpint.bf module on cluster. Can you please help where I am doing mistake. Thanks, Reetu +++++++++++++++++++++++++++++ 2). Looking for a breakpoint... Error: Master node received an error:Cannot reuse the filter 'filteredData0' because it is already being used by likelihood function 'lf', and the two likelihood functions impose different leaf-to-sequence mapping. Create a copy the filter and pass it to the second likelihood function to resolve this issue. Function call stack 1 : Construct the following likelihood function:filteredData0 ; givenTree1 ; filteredData1 ; givenTree0 ; Standard input redirect: Empty Associative List------- 2 : RunASample(individual) Standard input redirect: Empty Associative List------- |
Title: Re: How to mention the name of the nucleotide evolutionary model Post by RTuteja on Nov 19th, 2012 at 4:51am
P.S.- If I skip the KH-test then everything is working fine. Is this a bug or I am making some mistake?
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Title: Re: How to mention the name of the nucleotide evolutionary model Post by Sergei on Nov 19th, 2012 at 1:00pm
Hi Reetu,
I think this is a bug in the script. Let me investigate. Sergei |
Title: Re: How to mention the name of the nucleotide evolutionary model Post by yuda on Oct 4th, 2013 at 2:33am
Dear Sergei,
I was wondering whether you could fix the bug in the SBP script. Thank you, Haruo |
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