R help - Sep 2014 - package "ape" read.dna diploid input data

I am fundamentally not understanding something about how this is set up,
but after a few hours of googling I am going to ask and I apologize if its
quite basic. I have sanger data that I am reading into ape with read.dna.

x<-read.dna("/Volumes/Storage/file.phy", format =
"interleaved")

It has IUPAC codes in the data, which represent polymorphisms in a diploid
system. It is consistently read as haploid data, both in ape and when I
convert it for adegenet. What are you supposed to do to make the data read
as diploid? You can't just include duplicates of the sequences, it
doesn't
work. I've tried it with sequential alignments and .fasta files.

Thanks

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