Running Codeml On Unrooted Tree

Question

[GR]

Hello Everyone,

just a quick question- can I give an unrooted tree as an input to codeml or it is necessary to make your tree rooted for codeml analysis?

Thanks, Reetu

Answer 1

[David W]

From the manual (p. 15):

Whether you should use rooted or unrooted trees depends on the model, for example, on whether a molecular clock is assumed. Without the clock (clock = 0), unrooted trees should be used, such as ((1,2),3,4) or (1,2,(3,4)). With the clock or local-clock models, the trees should be rooted and these two trees are different and both are different from (((1,2),3),4). In PAML, a rooted tree has a bifurcation at the root, while an unrooted tree has a trifurcation or multifurcation at the root.

(you set the "clock or not" variable with the control file, PAML will throw a warning if you set the clock to 0 but still have a rooted tree)

[fransua]

At this point I have a doubt... Usually I use rooted trees with "clock=0", because I believe that it does not matter if you are not intersted in the estimations relative to the outgroup sequence (exact position of the root)... but I am not sure actually if this changes. Do you have an idea?

Answer 2

[hosseinv]

This is the answer in FAQ for PAML:

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.

[linhphuong89]

Hi, I am also doing an analysis for Dn Ds calculation using PAML. I also read the FAQ about whether I should use a rooted or unrooted tree or not. The point is the document is not very clear. It said that "for other models, neither the likelihood nor the parameter estimates are correct", thus I don't understand what does it mean by saying "for other models"? Does it mean that models other than codeml or baseml (although I thought that codeml and baseml are packages not models?)

Thanks a lot