Using PAML TO RECONSTRUCT ANCESTRAL PROTEIN SEQUENCES, BUT HOW TO ANALYSE THE RESULT?

[qianku...@gmail.com]

Hello everybody：

   I have  used PAML to reconstruct ancestral protein sequences ,but I don't know how to analyse the result. I looked the YANG's BOOK and saw the result in the "rst" file.But I don't know  what's the mean of "ASR( Ancestral Sequence Reconstruction )"and we should  how to  analyse the result  with the "ASR". 

   The file in the enclosure is my result "rst" file which there has a tree in,but I don't know the role of the tree. CAN anyone help me solve these question?

Thanks for all your replies.

 

Qiankun ZHANG

.

[Ruoqian Xiong]

The tree is a phylogeny generated by PAML when inferring ancestral sequences. (I assumed that you didn't input a tree file.) The program has to have a tree file first before it can generate ancestral sequences for you at each ancestral node on the phylogeny tree.

I hope this helps a little bit.

Best,

Amy

[zhang qiankun]

Hi Amy,

    I had input the tree file in the analysis and the attachment is the setting file.I want to use the Emiprical Bayes method to  make the ancestral sequence reconstruction . Does my setting file exist problems?

   Best,

   Qiankun

[Ziheng]

here is a start.

read

Yang, Z., S. Kumar, and M. Nei. 1995. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641-1650.

run codeml on the stewart dataset and try to duplicate the results in the paper.

ziheng