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How to run a dated Molecular Clock analysis? (Read 1608 times)
sam
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How to run a dated Molecular Clock analysis?
Jul 25th, 2007 at 12:43pm
 
Hi Sergei,

How do I run a dated Molecular Clock analysis (e.g.
GADatedClock.bf; DatedTipsMolecularClock)?  What
exactly do I need to do, to be able to run these?  I
loaded my nucleotide data file and newick file and got
an error message saying: "No date information found
for sequence 0. What units are the dates measured in
(e.g. months. This is only used for reporting the
results.)"?  Any suggestions?

Also, how do you change the molecular clock.bf file to get it to save (like we had to with the localmolclock.bf)?  We're trying to run some global molecular clock analyses.  It runs them, but again stops and asks for input.

Thanks, again, for all of your help.

-SAM
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« Last Edit: Jul 25th, 2007 at 11:50pm by N/A »  
 
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Sergei
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Datamonkeys are forever...

Posts: 1658
UCSD
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Re: How to run a dated Molecular Clock analysis?
Reply #1 - Jul 27th, 2007 at 11:56am
 
Dear Sam,

You need to have name your nodes in a special way (this is the convention used by Andrew Rambaut's TipDate), i.e. taxon name followed by a sampling date as in the following: ((((U69585s85,U69588s85),U69587s85),((U69590s90,U69593s90),U69592s90)),(U69586s8
5,(U69589s90,U69591s90)),U69584s85)

The numeric suffix of the taxon name is interpreted as the sampling date.

Cheers,
Sergei
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