raxml-ng ancestral reconstruction inserts amino acid codes into nucleotide alignment

[Josh D'Aeth]

Hi All

I'm having some issues running an ancestral state reconstruction using raxml-ng v1.0.3. 

I'm using the following command to reconstruct the ancestral states from bacterial genomes:

raxml-ng --threads 1 -model GTR+G --ancestral --msa dna.aln --prefix asr --tree tre.rooted

The input alignment is in nucleotide format, with only ACGT- characters present. However, the output .ancestralStates file contains what appears to be amino acid codes, mainly K and M , interspersed among the rest of the nucleotide sequence. Is there an option I'm missing to limit the reconstruction to nucleotide characters only? Any help with this would be gratefully appreciated. 

Cheers

Josh

[Alexey Kozlov]

Hi Josh,

those are not amino acids but ambiguous DNA characters in IUPAC code, see e.g.

https://www.bioinformatics.org/sms/iupac.html

Best,
Alexey

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[Josh D'Aeth]

Hi Alexey

Great, thanks for clearing that up!

Cheers

Josh