M2a_rel

[Suzanne McGaugh]

I had a quick question about how to specify the codeml.ctl file in PAML 4.7 to run the M2a_rel model. 

For the clade model, I have model =3, NSsites = 2. In the new version of PAML it says to do NSsites = 22 for the null model.

When I do this and leave everything else the same, I get the error, "Error: clade model should have model = 3 NSsites = 2 or 3.."

Thanks in advance for any information or advice you can offer.

Suzanne

[cajawe]

'model = 2' means that dN/dS differs among branches according to the labeled treefile.  dN/dS doesn't vary among branches under the M2a_rel model (it's a random-site model), so you should set 'model = 0' for M2a_rel.  

[Suzanne McGaugh]

Thanks- I think I was getting confused by the format of the output. I'll detail below, in case anyone else finds it helpful. Sorry if it is TMI.

CmC output:

site class             0         1         2

proportion        0.60326   0.02311   0.37362

branch type 0:    0.00917   1.00000   0.19446

branch type 1:    0.00917   1.00000   0.78591

I was thinking I would see this same layout, but with site class 2 for branch0 and branch1 being equal for M2a_rel

site class             0         1         2

proportion        0.60326   0.02312   0.37362

branch type 0:    0.00917   1.00000   = to branch type 1

branch type 1:    0.00917   1.00000   = to branch type 0

But I got this using m=0,  and it took until your email to realize that it is essentially the same thing as what I was expecting to see:

p:   0.59492  0.01520  0.38988

w:   0.00770  1.00000  0.27387

Thanks again!

[Ryan Schott]

The confusion seems to be between the difference between the random site models (model = 0) and the clade model (model = 3). The NSsites option sets the particular model within those categories (NSsites = 22 for M2a_rel and NSsites = 2 for Clade model C). It is a somewhat odd case where the null model (M2a_rel) of the clade model (CmC) is actually a random sites model and not a clade model.

The difference between M2a_rel and CmC is that CmC allows the third site class to vary between 2 or more branch types (which can be branch, clades
or some combination). Otherwise the models are the same (and this is what makes it a good null model).

I will add that when you run M2a_rel make sure to use an unlabelled tree (no branches/clade highlighted with #/$). Also make sure to run M2a_rel on
its own, and not in combination with other site models. Running it in combination (eg, NSsites= 0 1 2 22 7 8) seems to results in M2a_rel not working properly.

Hope this helps,

-Ryan

[Ziheng]

All good and thoughtful posts. Thanks.
I have nothing to add.
Ziheng