[Bioperl-l] PAML parsing: standard error?

[Jason Stajich]

Nope, it's not parsed.  feel free to add it and post a patch...

On May 2, 2005, at 5:13 PM, Edward Chuong wrote:

> Hi,
>
> Has parsing the standard errors for pairwise comp been implemented
> yet? Can't seem to figure out how to retrieve them.
>
> (if getSE = 1, the bottom of the file would look like this)
>
> pairwise comparison, codon frequencies: F3x4.
>
>
> 2 (PM_BWp0020A12f/1-633) ... 1 (mouse/1-630)
> lnL =-1299.951893
>   0.88536  2.62235  0.89353
> SEs for parameters:
>   0.08133  0.51260  0.19693
>
> t= 0.8854  S=   178.0  N=   443.0  dN/dS= 0.8933  dN= 0.2854  dS= 
> 0.3194
> dN = 0.28536 +- 0.03182   dS = 0.31943 +- 0.05807 (by method 1)
> dN = 0.28536 +- 0.03182   dS = 0.31943 +- 0.05807 (by method 2)
>
> Thanks!
> -Ed
>
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--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/