Protein Sequence Example and Errors While Uploading Nexus File

[Shoaib Khan]

Dear BEAST Team,

I am currently working on phylogenetic analysis using protein (amino acid) sequences and would like to use BEAST for this purpose. However, I’ve encountered several challenges:

1. Lack of Protein Sequence Example:
   I could not find any example or template file demonstrating the use of amino acid sequences in BEAST. All available examples seem to focus on nucleotide data. Could you please share a sample dataset or .xml file for protein sequences?

2. Errors with Nexus File Exported from MEGA:
   When I export my alignment (in amino acid format) from MEGA into Nexus format and attempt to load it into BEAUti or BEAST, I encounter multiple errors, including:

   •   "ERROR PARSING --- " 

   •   "ERROR PARSING IMPORTED FILE DATATYPE"

   • " ERROR PARSING IMPORTED FILE NUMBER OF TAXA DOESN'T MATCH NTAXA FIELD"  

   I would appreciate your guidance on the correct formatting for protein alignments and how to import them into BEAST properly. Are there specific symbols or settings required in the Nexus file header or data block?

Thank you in advance for your assistance. I look forward to your guidance.

Best regards,
Shoaib Khan
Comparative and Evolutionary Genomics Lab. 
National Center for Bioinformatics Islamabad, PK

[Walker Orr]

I suspect the issue

• " ERROR PARSING IMPORTED FILE NUMBER OF TAXA DOESN'T MATCH NTAXA FIELD"  

may be with your sequence names. there cannot be any spaces in any of the sequence names, as this will prevent treeAnnotator from correctly identifying the number of taxa in your dataset. You can ask gemini to write you a script to fix this in your .trees file on disk, so you don't have to redo your beast run.

-Walker

[Walker Orr]

I am having the same issues. When reconstructing ancestral sequences (or not, haven't tried without yet) treeannotator will not parse my tree file and gives the same error message as Dr. Khan: ERROR PARSING IMPORTED FILE NUMBER OF TAXA DOESN'T MATCH NTAXA FIELD.

On Thursday, June 19, 2025 at 2:59:39 PM UTC-4 Shoaib Khan wrote: