error in tree file

[Natasa]

Hi,

I am trying to run codeml in pamlX. However,  I got an error message "Species PPARGC1B?". I used tree file made by Phyleasprog, which is in .nhx format. I tried also with trees made with MEGA (tree.nwk)  and PhyML (tree.nwk), but I was getting similar messages (Error: "Species 1.0000?"). I assume the problem is in the tree file (I ran the seq file in YN00 and it was read correctly).

I also tried to remove support values as suggested in one of the earlier posts, but that didn't work either.

Here are the seq and tree files if anyone has suggestions how to fix this.

Thanks for any input!!!

Natasa

[Adrián Goig Serrano]

Hi Natasa, I think I know the problem. Trees in newick format exported by MEGA have the following structure:

((((((((CTXM11:0.00478346,CTXM54:0.00119232)0.1590:0.00000000,CTXM3:0.00000000)...etc

I found that PAML expects a specie just before " : " so in this case "0.1590" will be interpreted as a specie.

Yo can fix that problem just removing this values and leaving the tree with the following structure:

((((((((CTXM11:0.00478346,CTXM54:0.00119232):0.00000000,CTXM3:0.00000000)...etc

OR simple alternative is to use FigTree. Just open your newick formatted tree and then export in newick format too. FigTree will remove this values and PAML will work fine (I tried it).

PD: I'm a bioinformatics student and I don't work in this field. I just found this way to fix this issue. So forget me if this is not the perfect solution. If it works for you, maybe you can add to the topic of this thread a [SOLVED] so the rest of the community could take advantage of the information.

Greetings,
Adrián Goig

[Adrián Goig Serrano]

By the way, I'm working with PAML- 4.7 on Linux

[Natasa]

Hi Adrian,

Thanks for suggestion! I will try it and will let you know if it works:-)

Natasa

[Denis Odokonyero]

Hey Natasha, 

I don't know if Adrian's suggestion worked for you already, but, I was having a similar error and tried Adrian's suggestion of re-saving in a newick format (manually removing support values would not have worked for me, I have a lot of sequences), but it did not help. I too thought the problem was my tree, but it turns out it was the sequence file. After a couple of frustrated attempts, I changed it into a .phy format and viola! I don't know if we had the exact same issue but this worked for me. I hope it helps somebody else as well. Good luck! 

[Ziheng]

One thing is that both the sequence file and the tree file are plain text files, so you can edit them using a text editor.
Have a look at the examples in the package and get to kow the basic format. Then you can open and inspect the files generated by the various programs you are using.
Ziheng