I have a data set with diploid seqeunces that were converted to IUPAC ambiguity codes for heterozygotes, e.g.
Mex1 ATWGGCYACT is het for A/T at pos 3 and C/T at pos 7
Mex2 ATWGGCYACT " " "
Mex3 ATAGGCTACT is homozygous at pos 3 and 7
When I convert back to data format appropriate for IMa2 , two lines per ind.:
I lose phase information ( for Mex1, does A in pos 3 go with T in pos 7 or C?). Will this be a problem when running IMA2 or is each variable site treated more or less independently within a sequence?