Does snp-dists 0.2 count the number of Ns in an alignment too? Or does it ignore them?

tseemann / snp-dists

Pairwise SNP distance matrix from a FASTA sequence alignment

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Does snp-dists 0.2 count the number of Ns in an alignment too? Or does it ignore them? #18

Closed slvrshot closed 6 years ago

slvrshot commented 6 years ago

Question is basically the title. I have an output file from Gubbins were recombinant regions in the core genome have been removed. These recombinant blocks appear as Ns in the alignment.

Please help.

tseemann commented 6 years ago

It doesn't care what letters you have in your alignment. If they are different, it counts. It was designed for true core SNP alignments only. Future versions (some in github currently) will address this. You may want to look at disty instead: https://github.com/c2-d2/disty