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simulation form an ancestral sequence (Read 1688 times)
ofedrigo
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simulation form an ancestral sequence
Oct 24th, 2006 at 7:50am
 
hi,

I have a dataset from which I estimate my ML parameters. I would like to simulate many dataset from it but starting from the ancestral sequence of my original dataset. How does the simulatedataset function work? does it start from a random sequence with a similar base frequency or does it start from the most ancestral sequence of the original dataset? is there a way to do specifiy these two options?

thanks,

Olivier
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Sergei
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Re: simulation form an ancestral sequence
Reply #1 - Oct 24th, 2006 at 11:21am
 
Dear Olivier,

At the end of your analysis (or after you've reloaded a fit), you will have a tree with attached models to simulate from (call it myTree).

The function you want is Simulate. You may need to tweak the characters option if your data is not nucleotides. Take a look at the documentation of the 'Simulate' command.

Code:
characters = {{"A","C","G","T"}
			    {"1","","",""}};


DataSet sim = Simulate (myTree,eqf,characters,ancestralString);
 



ancestralString will be where you pass your root sequence, and eqf is the vector of base frequencies (which won't be used if you pass an actual string as the 4th argument).

Cheers,
Sergei
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