Error: Seq # occurs more than once in the tree

[Maria Eduarda Lacerda]

Hello everyone, I'm new in paml and I’m having doubts about the program.
I tried running a site model analysis, and the program signalizing that has an error because it’s supposed that some sequence occurs more than once. Still, I certainly have different sequences, but with just a few sites various in sequences.
Does anyone know a way to solve this?
Thank you so much! 

[Janet Young]

hi,

The error message might be telling you that the sequence NAME that occurs more than once rather than the sequence itself - can you check for that?

You say only a few sites vary: you might also want to think about whether you have enough variation in your alignment for PAML to make sense.    Is it within-population data, or across-species?

Janet

[Y Z]

Hi,

I have the same problem here. I have checked the seq names and all of them are unique. When I use gene tree, it worked, but when I use species tree, the problem occurred. 

What would be the problem?

Yang

[Sandra AC]

Hi there, 

You may try to debug the problem by looking at the following:

• Have you made you sure that you have a PHYLIP header with the same number of species in both the tree file and the alignment? E.g., for 1 tree with 4 taxa and an alignment of 120bp with 4 taxa, the headers for both tree and alignment files, respectively, would be `4 1` and `4 120`. If there is a mismatch between the number of species (i..e, `4` in this example), that would cause a problem.
• If you have included a PHYLIP header, have you made sure that you have as many taxa as what you indicate in the header? If you have indicated `5 1` in the tree file but your tree file has 6 taxa, there would be a problem -- same applies to the alignment.
• Have you made sure that the same tag IDs have been used in the alignment and the tree files? A mismatch would stop the analysis.
• Have you made sure that you have not used the same tag at least twice in the tree and the alignment files? E.g., "(sp1, (sp1,sp2));" has tag "sp1" repeated twice. That would cause a problem too.

Cannot think of anything else without looking at the files... If nothing of the mentioned above works, you can share your tree and alignment files to see if we can troubleshoot it!

Hope this helps!
Sandra

[Bruce Onisko]

I had the same problem.  But 2 sequences did NOT have spaces after the header.

I added 10 spaces to each and the problem went away.

Very strange.  I did not think I had any spaces after my headers.  just carriage returns.  Maybe I had tabs?

Buce

[Sandra AC]

Hi Bruce,

Thanks for your message! I am not sure how your sequence alignment file was formatted, but it seems that the sequence was not separated from the taxon name by at least two spaces or, as you pointed out, carriage returns may have been in conflict with the UTF-8 format (e.g., "\r", "\M"; they may appear on your files if they were created in Windows-based system). For more details on how input data need to be formatted, you may want to check the PAML Wiki on GitHub. Please let us know if you have experienced any other issues with regards to the input files!

Hope this helps!

All the best,
Sandy