Question on rooted tree warning

[Linh Phương Nguyễn]

Hi,

I am trying to calculate Dn Ds using codeml. I use model = 2 to calculate different Dn Ds for different groups of species, and method = 1. The point is since I thought I only need to calculate Dn Ds value, I would not care about the clock and I set it = 0. But the result give me a warning : " This is a rooted tree. Please check!". I have read the FAQ on PAML but it is not really clear. It said that: " For most models, the likelihood values are still correct even if you use a rooted tree, but the lengths of the two branches around the root are not stable, as only their sum is estimable. For other models, neither the likelihood nor the parameter estimates are correct. So really you should heed the message and use an unrooted tree in the analysis."  But it does not state what are those models. 

Plus I am using method = 1 and in the tutorials it said that method = 1 does not work under the clock model. Therefore, I do not understand if I should seriously take into account the warning.

Thanks a lot.

[Ziheng]

There are two things, clock vs no clock, and rooted and unrooted trees.
For your analysis, it sounds like clock = 0 is the right choice, but probably you have a rooted tree and you should edit it to make it become an unrooted tree.
An unrooted tree will have the outmost pair of parentheses grouping three species or clades.

((1,2),3); is rooted.
(1,2,3); Is unrooted.
For further info, see or search in the doc pamlDOC.pdf.
Ziheng