Does phase matter in diploid sequence data?

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LPlough

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Oct 12, 2015, 1:23:07 PM10/12/15
to Isolation with Migration
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.:

Mex1 ATAGGCTACT
Mex1 ATTGGCCACT   

Mex2 ATAGGCCACT
Mex2 ATTGGCTACT

Mex3 ATAGGCTACT
Mex3 ATAGGCTACT

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? 

Thanks,
Louis
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