How to create a tree file

[张磊]

Hi,

I want to use PAML to analysis the positive selection sites for several genes, but when i use the MEGA soft to produce a tree file, the program baseml and codeml couldn't recongnise and analysis the data. So, Would someone tell me how to create a tree file which can be used in PAML? Thanks!

[Feifei Zhang]

Hello,

I think the tree file generated from MEGA should work. Which tree file format did you use? Double check the tree file name in the control file is correct. Also, what error message did you get?

Good luck,
Feifei

[Zehra]

Hi,

I ve been trying to work with the newick format generated by MEGA 5. For one sequence PAML works fine with the given format, however, with rest of the sequences it  gives me this error:

# seqs in tree file does not match. Read as the nexus format.

Even on trying the nexus format, it doesn't read the first of my sequences in the tree file.

[dayan...@gmail.com]

Zehra:

I had the same issue, I over came it by using the mega tree file and open it with the software figtree 1.4.0 and then exporting it in nexus.  then all you have to do is make sure that there are no blocks other than the actual tree information.

Good luck

[Ziheng]

I have no experience with mega.
Nevertheless all the files are text files so you can use an editor to open them and look at them. Look at some example tree files in the paml package, and then look at the trees created by mega.
Ziheng

[Peter Atanackov]

In MEGA open your tree in Tree Explorer, in the top bar click "Display only Topology", export the tree in Newick format. Open the same tree in FigTree, go to Export trees and chose again Newick format (it changes the tree). After all this is done open the tree in a text editor and delete all " ' " symbols (yes this symbol -> ' ), use the replace tool for a quick fix. It should work now.