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ASR (Read 3113 times)

edison YaBB Newbies Offline Curious HyPhy user Posts: 2 Gender:	ASR Apr 15^th, 2012 at 3:47am When I run the ASR analysis, I have to choose a name as the root of the tree. Whether the different roots affect the results? When the process was finished, the results show me some nodes. What is meant by node 0 ?
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: ASR Reply #1 - Apr 18^th, 2012 at 3:06pm Hi Edison, NodeX, where X is a number, is a name assigned to an internal node by HyPhy automatically. Node0 is the root node (always). Datamonkey displays a tree on the results page which shows internal node labels to help one navigate the results. Sergei
Back to top	Associate Professor Division of Infectious Diseases Division of Biomedical Informatics School of Medicine University of California San Diego WWW IP Logged

edison YaBB Newbies Offline Curious HyPhy user Posts: 2 Gender:	Re: ASR Reply #2 - Apr 20^th, 2012 at 10:44pm Dear prof. Sergei Thanks for your reply. You forgot to answer me the first Q. When I run the ASR analysis, I have to choose a name (gene） as the root of the tree. Whether the different roots affect the final results?
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Sergei

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Re: ASR
Reply #3 - Apr 23^rd, 2012 at 1:23pm

edison wrote on Apr 20^th, 2012 at 10:44pm:

Dear prof. Sergei
Thanks for your reply. You forgot to answer me the first Q. When I run the ASR analysis, I have to choose a name (gene） as the root of the tree. Whether the different roots affect the final results?

Under time reversible models, the location of the will not affect likelihood calculations, and by extension -- the reconstruction of ancestral sequences. The location of the root matters, of course, for how the internal nodes are arranged and names.

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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