please, does anyone know why I get not calculable "values" for certain pairwise alignments when calculating synonymous and non-synonymous substitutions? (both when using just number of differences and distances, however the proportion of n/c differs between the models used).
I had this problem if just a single codon was aligned, eg. folowing alignment:
If number of differences was calculated using Nei-Gojobori model, then:
[ 1 2 3 4 5 6 ]
 n/c n/c
 n/c n/c n/c
 n/c n/c 1.000 n/c
 n/c n/c n/c n/c n/c
I could understand that there is a problem for the pairwise align. where there is more than one substitution between the two codons, but the n/c is present even for single-substitution pairs.
Thanks very much if someone can help.
Mega:not calculable values for syn/nonsyn substitutions
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