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How to (Read 1529 times)

bkfung1398

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How to
Nov 15^th, 2007 at 4:22pm

Hello,

Iam trying to perform a DatedTipsMolecularClock analysis on a nucleotide alignment. When I enter the alignment file I recieve a message saying ""No date information found for sequence 0". Do I have to enter the sequece file in newick format? or Do I have to make a tree and then enter it into the analysis?
Also I am aware that I have to name my nodes via Rambaut's TipDate convention. Do you have any suggestions on how to do this or recommend a manual which can show me precisely how to name the taxon and its sampling date and where in Hyphy?

Thanks
Branden

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Art Poon

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Re: How to
Reply #1 - Dec 17^th, 2007 at 3:38pm

Hi Branden,

Can you please provide an excerpt from your sequence file? You will need to provide a tree if one is not included in your alignment file. The tree has to be rooted. A regular expression for the TipDate naming convention is "_[0-9]+", in which the second integer term corresponds to the number of calendar time units associated with that sequence.

Best,
- Art.

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Question: How to run DatedTipsMolecularClock
To run DatedTipsMolecularClock 1 (50.0%) Or NOT to run DatedTipsMolecularClock 1 (50.0%) That is the question 0 (0.0%) Total votes: 2 « Last Modified by: Sergei on: Dec 17^th, 2007 at 3:45pm »