(Cc. to r-sig-genetics)
I'm going to modify the algorithm in haplotype.DNAbin() as follows:
1. Find the sequences that are exactly identical, so that, eg, the 3 sequences:
A-
AR
AA
would be treated as different at this step.
2. Substitute the leading and trailing "-" for N (thus keeping the al
Hi Hirra,
The assignment is not random, it follows the order of the sequences in the data:
- Seqs. A and B are compared and found to be identical so they are both
assigned to haplotype I.
- Seq. C is compared to haplotype I (effectively seq. A) and found to be
different so it is assigned to hap
Hello,
I am using the pegas R package to assign sequences into haplotypes.
I recently tried out a test examples with 4 sequences. 2 of the sequences (A
and B) are identical, 1 sequence (Seq C) differs from these at only one
position (pos 648).
The 4th sequence (Seq D) is identical to all but sh
