9.3 years ago by
Santiago de Compostela, Spain
the phase status of an allele takes into account in which chromosome pair has been found. as far as I know, the main reason to use allele phasing information is to increase the correctness of the haplotypes and haplotype blocks inferred from them. it makes sense to name all allele pairs sorted in the same way once you know which allele pair is on which chromosome pair, because if you have all this information sorted you'll be able to easily build haplotypes by dealing sequentialy first with first allele bases only and then with second allele bases only.
trying to be a little more visual (and simplistic too, so please all basic geneticists accept my apologizes in advance), take the table from the webpage you've mentioned:
IND, id1, id2, id3, id4, id5
rs1, AT, TT, ??, AT, AA
rs2, GC, CC, GG, CC, CG
rs3, CC, ??, ??, CG, GG
rs4, AC, CC, AA, AC, AA
if you look to individual 1 (id1) you will have 2 different haplotypes: AGCA (from first chromosome pair) and TCCC (from second chromosome pair). this information wouldn't be known if genotypes were unphased, in which case other haplotyping algorithm should be applied.
