FastTree error: Non-unique name 'xxxxx' in the alignment

Question

[eedeaguiar]

Hey, so I am trying to build a phylogeny, but I am running into this error for FastTree, and I do not see much about it online. Does anyone know if I could use a program to rename all names to be unique in my alignment, or is it a fundamental error that shouldn't have happened in the first place.

For some context about my data: Trying to generate a phylogeny of 4 subspecies and an outgroup. Whole genome data and I work on an HPC.

• Retrieved single copy orthologues through OrthoFinder
• Aligned them with MAFFT
• Put the alignment of orthologues into FastTree

I was thinking of trimming my alignments with BMGE, but have yet to do it.

Let me know!

Answer 1

[Mensur Dlakic]

Non-unique name 'xxxxx' in the alignment

The error is self-explanatory: you have more than one sequence in your alignment named xxxxx. As to why, it is difficult to tell. This problem wouldn't have been created by MAFFT because it simply uses the provided sequence names. Most likely it happened while you were collecting sequences.

Fixing it should be easy if you have only 4+1 sequences and can be done manually. Just make sure all of them have different names.

Trimming alignments with BMGE is generally a good idea for wide alignments.

[eedeaguiar]

Ah okay good to know, thank you for your response. To clarify, I don't have 4+1 sequences, I have 34,000 sequences. I will look into this further