MATLAB: Seqpdist Kimura “method not available for amino acids” even though working with nucleotides

Bioinformatics Toolboxseqpdist

Hi, I am trying to use the seqpdist function in matlab (Matlab R2019a, academic license) to compute the pairwise distance between two sequences, with the Kimura method, however, I get the following error even though I am working with nucleotides, not amino acids:
Error using seqpdist (line 335)
Distance method not available for amino acids.
below a 2-line MWE:
ex = {'aagt', 'aatg'}
seqpdist(ex, 'Method', 'Kimura')
Error using seqpdist (line 335)
Distance method not available for amino acids.
I also tried with 
ex = {'ACGT', 'AATG'}
ex = ['ACGT', 'AATG']
And got the same error. Can someone explain?
Thanks in Advance!

Best Answer

As Geoff points out in the comments, the problem is that several of the default option values don't work for the Kimura distance method. By default, seqpdist assumes that you're using amino acids and that indels are scored. I confirmed that the following works for your example:
ex = {'aagt', 'aatg'};
seqpdist(ex, 'Method', 'Kimura', 'Alphabet', 'nt', 'Indels', 'complete-del')
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