[Biojava-l] dN/dS ratio calculation biojava

[Andy Yates]

Hi JP,

No there isn't a class to calculate dN/dS. At a basic level dN/dS is a
very easy ratio to calculate if you take the very basic approach of
sequences of exact lengths. The basics of it are available from:

http://pubmlst.org/software/analysis/start/manual/dsdn.shtml

The best package I know of to calculate the rates though is codeml. It's
a very awkward program to run but it can be done & will produce the best
results. I can say for sure that the Ensembl Compara team use it to
calculate dN/dS rates for their homologous protein sets.

Hope that helps,

Andy

P.S. I say all of this from personal experience when I wrote a very
basic calculator using BioJava (and I don't know where the code got to).
The amount of work to produce that code vs. running a third party
application just makes it more cost effective to go for the 3rd party app

JP wrote:
> Hi there - is there a class or method which finds the dN/dS ratio
> (nonsynonymous/synonymous rate ratio) for two sequences ?
> 
> Many Thanks
> JP
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