I noticed that there are a lot of '?' symbols in the amino acid translation of my nucleotide sequences.  I am wondering why this is and if this would affect the Datamonkey analyses I'm running.

My job ID is 405622433913805.1.

Any input would be appreciated.

Justin

Hi Justin,

The '?' symbols you see are caused by the fact that in your nucleotide alignment, gaps span codon boundaries --  for example around nucleotide position 1125:


AG---AAAA
AA---AAAA
AG---AAAA
AG---AAAA
AG---AAAA
...


HyPhy will read this as codons AG-, --A, AAA for sequence 1 for instance, and both AG- and --A map to "ambiguous" (i.e. ?) amino acids.

I would check your alignment to make sure the gaps are correctly placed, because they could affect Datamonkey inference.

Best,
Sergei

Ahh...makes sense. 

Thanks so much for looking into that for me!

Best,

Justin