Help For Paml About The Positive Selection

Question

[Zhipeng Li]

Hi everyone!

this is the first time for questions at biostar, so i am pleasure to ask and discuss questions at biostar.

I am planning to conduct the PAML software for detecting the possible positive site with animo acid sequences. But i still can not understand how to design the branch model or site model by the control file, although i have read the document of PAML.

You are welcome to discuss!

[2184687-1231-83-]

Do you want to find positions in the sequence under positive selection (sites model) or branches in the tree under positive selection (branch model) or a combination of both (branch-sites model)?

[Zhipeng Li]

i want to find positive position under branch and site model .But i have not got how to design the control file using the animo acid sequences.

[Casey Bergman]

Hi Zhipeng - please try to formulate a question that can be answered directly, see the following link for tips: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002202

[Joseph Hughes]

Sorry but your question is really too general for anybody to be able to help you. It sounds like you haven't even attempted to read through the manual or try any of the tutorials http://abacus.gene.ucl.ac.uk/software/paml.html. To start with the analyses is conducted on the codon based alignment and not the amino acid alignment.

Answer 1

[Martombo]

1) to use a branch model:

• if you want to let w free to have different values in each branch, you have to set the variable model = 1 (this is not usually a good choice because you may overfit the data and have meaningless results).
• you can group some branches together and associate them with the same w which can either be fixed or not. in this case you should set model = 2. by doing so you lose resolution but the results you get are more likely to be relevant (to know how to group branches you can have a look at the example/lysozyme/)

---

2) to use a site model set the variable model = 0 and use the variable Nssites to choose the models you want to evaluate (e.g. Nssites = 1 2). you can then compare two models by means of the likelihood ratio test, to see which one can best explain the observed data.

---

these analyses require codon type sequences (seqtype = 1). all the concepts and statistics you can find in paml are widely discussed in the book "computational molecular evolution". I would also suggest you to formulate an hypothesis about your data, before running many different analysis. if you don't know what you are looking for, you may find anything by chance!

Answer 2

[Zhouwp]

try its examples first.