PEGAS: why did pegas not assign separate haplotype

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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