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Methodology Questions >> How to >> model designation http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1151432418 Message started by cheilarocha on Jun 27th, 2006 at 11:20am |
Title: model designation Post by cheilarocha on Jun 27th, 2006 at 11:20am
I would like to know the 6 character designation of the model GTR-G. Thank you!
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Title: Re: model designation Post by Sergei on Jun 27th, 2006 at 12:25pm
Dear cheilarocha,
wrote on Jun 27th, 2006 at 11:20am:
You can use the string 012345 to designate GTR (6 different rates). The '-G' part is specified in another dialog (site-to-site rate variation), where you would choose Gamma (we actually recommend the Beta-Gamma extension, as it nearly always outperforms the Gamma). Which analyses are you trying to specify the model for? Cheers, Sergei |
Title: Re: model designation Post by cheila on Jun 27th, 2006 at 3:54pm
you are fast! thank you!
I am performing the analyses of positive selection with NielsenYang method but the best model for my samples (model test performed with PAML) is GTR-G. what should I do? use GTR (012345) or another? all the best! Cheila |
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