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DIVERSITY/DIVERGENCE (Read 1182 times)
phylo
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DIVERSITY/DIVERGENCE
Aug 8th, 2009 at 10:10pm  
Hi Sergei,

I have a question regarding how does HYPHY calculate diversity and divergence from a set of sequences. Is it from for instance the JC distance? Because this would seem a very simplistic way to calculate such parameters right? So just wondering is the ML method more robust. Thanks in advance,
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Sergei
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Re: DIVERSITY/DIVERGENCE
Reply #1 - Aug 10th, 2009 at 11:44am  
Hi phylo,

Most generally, HyPhy will use the ML fit. It can also use standard ML variance estimators to place confidence intervals on the estimated quantities.

Sergei
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