10.2 years ago by

Scotland, UK

I posted the question on the UCL discussion board for PAML and got an answer from Ziheng Yang (see below).

I am conducting pairwise analyses in codeml with the getSE option and I get the following output:

```
lnL =-3838.516740
2.10195 1.24365 0.08719 (=> What are these values?)
```

the three values here are t, kappa and w. They are duplicated below in the "formatted output". For example t = 2.1020. You can ignore this line of output and look at the output below, or look at the program documentation doc/pamlDOC.pdf.

```
SEs for parameters:
0.26108 0.18309 0.01564
t= 2.1020 S= 405.5 N= 1355.5 dN/dS= 0.0872
dN= 0.2054 dS= 2.3560 dN = 0.20539 +- 0.01576 dS = 2.35601 +- 0.37598 (by method 1)
dN = 0.20539 +- 0.01576 dS = 2.35601 +- 0.37598 (by method 2)
```

What is method 1 and method 2? Does the +- value correspond to the SE of dN and dS?"

They are two different ways (both approximate) for calculating the variance-covariance matrix. I am not sure whether they are explained somewhere, for example, in the documentation. If you are technically sophisticated, you can look at the routine VariancedSdN() in the file codeml.c, and also Appendix B: the delta technique in Yang (2006 Computational Molecular Evolution). Here are some notes in the program, which explains the basic idea.

This calculates the covariance matrix of dS & dN, using the difference approximation, from the covariance matrix of t and omega (vtw). com.kappa and com.pi are used. Sampling errors in parameters other than t and omega, such as kappa and pi[], are ignored.

JacobiSN = {{dS/dt, dS/dw}, {dN/dt,dN/dw}}

And yes, the +- values are the SEs.

ziheng yang