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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy feedback >> Using BS-REL to perform molecular dating analysis http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1383745432 Message started by rss on Nov 6^th, 2013 at 5:43am

Title: Using BS-REL to perform molecular dating analysis
Post by rss on Nov 6^th, 2013 at 5:43am

I've been trying to perform the molecular dating analysis from the coronavirus paper ("A Case for the Ancient Origin of Coronaviruses," Wertheim et al., 2013) on my dataset. I've run the BranchSiteRel batch file on my data, but am not sure how to interpret the output. Are the mixtureTree.node.t1 parameters in the output .fit file the branch lengths in substitutions per site? Is there a way to visualize the tree with branch lengths given the .fit file? Any advice will be much appreciated!

Title: Re: Using BS-REL to perform molecular dating analysis
Post by Joel on Nov 12^th, 2013 at 11:30am

The branch lengths are not the .t parameters. They are a function of the .t paramters, the omegas, their proportions, and the substitution matrix. The most up-to-date version of the Branch-Site REL batchfile should export a tree with branch lengths in standard out. If you are not seeing this, please let me know.

Title: Re: Using BS-REL to perform molecular dating analysis
Post by rss on Nov 12^th, 2013 at 7:20pm

Thank you so much for the helpful reply--your answer made the program output much clearer to me.