Hello,

Recently I've been encountering issues with some codon alignment files I'm inputting into FUBAR, which yields the following error message -

Error: Incompatible dimensions when trying to add or subtract matrices: first argument was a 4x3 matrix and the second was a 20x3 matrix.

Further, I tried other HyPhy algorithms to check if errors are always thrown,  and I receive error messages such as the following -

DataSetFilter 'filteredData' contains non-standard data and SelectTemplateModel is not applicable.



There seems to be no difference that I can see between files that work and files that do not work (especially since they were produced by the same pipeline). All are codon alignments, and I initially suspected that the issue might be due to ambiguous data (many N's in the alignment), but I have never had an issue with having ambiguous residues in the past. Perhaps there are too many in the alignments that give errors?

Any light you could shed on why I'm receiving this error would be appreciated!

Best,
Stephanie

Hi Stephanie,

Sorry for taking a while to respond. It seems to me like HyPhy is sometimes reading your nucleotide data as aminoacid data. This can happen if there are a lot of N's in the nucleotide alignment. Two possible solutions are:

1. Use rhe NEXUS file format -- you can specify the type of the data explicitly
2. Replace N's with ? in your input data

Sergei