evolverNSbranches tree paramenter

[sumei zhou]

Hi, authors,

I'm using evolverNSbranches to simulte codon sequeuce under the branch model. I have some confusion about how to set the parameter of MCcodonNSbranches.dat :

I run the codeml branch model use the true sequence, and I got the ML tree and omega value of each branch,  I'm not sure:

(1) tree length:  I guess it's correct to get this parameter  from codeml output file? 

(2) tree:  should I use the ML tree or my species tree with accurate branch length?  There is a big difference between these two trees.

Your reply means a lof for me, thank you for your patience!

[Sandra AC]

Hi there!

Thanks for your message! Please find below the answers to your question:

• You can use "-1" for the tree length if your tree has absolute branch lengths; this option is a scale factor used to multiply.
• This is actually up to you and shall always depend on the type of simulation you are considering according to your hypothesis :)

Please remember to check the PAML Wiki, where there is a section for Evolver with all the details for each of the variables to be included in the control file that you need to know! You shall also find the links to various examples for the control files depending on whether you are to simulate codon, nucleotide, or amino acid data.

Hope this helps!

All the best,
Sandy