[Bioperl-l] PAML parsing: standard error?

[Edward Chuong]

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