[Biopython] parsing baseml result file information

[WU]

Dear all,
I am using biopython with the module of Bio.Phylo.PAML to parse result information obtained by baseml program. in the default result file of mlb I can see two parameters of ntime and np in the line of lnL like following:
lnL(ntime:  7  np: 13):  -1900.632719    +0.000000

When running codeml  for positive selection with branch-site model I know I need to use the values of np of different models to calculate the freedom of chi square distribution. So I think the np value are also useful in baseml. But in the baseml.Baseml() method, these two value are not included. I check the website of http://biopython.org/wiki/PAML and failed to find these information.
So my question is: 1) whether these two parameters of np and ntime are useful in calculating the p value with chi-square distribution, and 2) how to get these informtaion in the baseml.Baseml() methods.

Best wishes,

Qi WU





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