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Using BS-REL to perform molecular dating analysis (Read 2583 times)
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Curious HyPhy user

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Using BS-REL to perform molecular dating analysis
Nov 6th, 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!
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Joel
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Feed your monkey!

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Re: Using BS-REL to perform molecular dating analysis
Reply #1 - Nov 12th, 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.
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Re: Using BS-REL to perform molecular dating analysis
Reply #2 - Nov 12th, 2013 at 7:20pm
 
Thank you so much for the helpful reply--your answer made the program output much clearer to me.
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