CODEML parameter (p,w) estimate errors

[Yuri]

Hello,

I've been running some tests on synthetic data using CODEML and I've encountered some concerns with omega and category weight estimates when branch lengths are estimated. This problem is reproducible and consistent in PAML 4.10.10. From what I've tested, this does not seem to occur in PAML 4.10.9 with the same datasets. M2a and M8 seem to be most affected.

For example, running M2a (NSsites = 2) I can produce the following estimates from the same dataset, running the same .ctl file.

4.10.10

MLEs of dN/dS (w) for site classes (K=3)

p:   1.00000  0.00000  0.00000
w:   1.00000  1.00000 42.40770

4.10.9

MLEs of dN/dS (w) for site classes (K=3)

p:   0.40383  0.00000  0.59617
w:   0.82781  1.00000  1.99162

[Sandra AC]

Hi Yuri,

Thanks for your message! In order for us to be able to reproduce and troubleshoot this issue, could you please share the control files and input tree and sequence files you have used?

Thanks in advance!
Sandy