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 ?

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

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?

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.