Hello,
I have a question about the pegas haplotype algorithm and would be grateful if
someone could explain.
I used pegas haplotype() on a set of sequences. I then manually aligned and
looked at the sequences within each haplotype. For one haplotype I noticed
something odd (see image below)
Although there was a single bp difference at the highlighted position ,these
sequences had all been assigned as one haplotype. I understand that for the 3rd
sequence because there are gaps at this highlighted position this can lead it
to be pooled with others, but I do not understand how sequence 1 and 2 can be
in the same haplotype?
I would be grateful for any guidance,
GBSP11539-19|Ophlitaspon[1]
AATACTGCATTTTTTGACCCTGCAGGGGGAGGAGACCCCATTTTATATCAACATTTATTT 660
GBSP11518-19|Ophlitaspon[2]
AATACTGCATTTTTTGACCCTGCGGGGGGAGGAGACCCCATTTTA--------------- 645
GBSP11504-19|Ophlitaspon[3]
AATACTGCAT-------------------------------------------------- 580
GBSP11512-19|Ophlitaspon[4]
AATACTGCATTTTTTGACCCTGCAGGGGGAGGAGACCCATTTATATCACTTTATTTGTT- 659
**********
Best wishes
Hirra
University of Manchester Student.
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