How to set subs. model without +G in CODEML

[Sishuo Wang]

Dear all,

I wondered if anyone knows how to set the model not under +G for CODEML.

I see the option "ncatG = " in codeml.ctl. However, when I set it to 1, I got the following msg,

error: ncatG

I think it's still run under model without +G, right? I think an alt. way is to set "fix_alpha = 1, alpha = 1000, ncatG = 2", which didn't yield any err. msg. and indeed generated very very similar result. I was using v4.10.7.

Any suggestions? Thanks so much!

best,

sishuo

[Sishuo Wang]

Sorry, I don't think ncatG = 1 is a legal setting in PAML v4.10.7 thus no output is generated. Perhaps the only way is to the alt. way as suggested in my original questions?

thanks,

sishuo

[Sandra AC]

Hi Sishuo,

Following the PAML documentation (p. 22; but same settings would apply to CODEML), perhaps you may want to try `fix_alpha = 1` and `alpha = 0` (0 means infinity)? To this end, you will have a single rate for all sites.

Hope this helps!
Sandy

[Sishuo Wang]

Hi Sandra,

Thanks! I see: fixing alpha to 0 represents infinity and it should be the professional way, although alpha=1000 (big enough) would lead to almost the same result.

best,

sishuo