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Mark fry

seqpdist: missing data vs gaps

Asked by Mark fry
on 30 Jan 2013


I'm using seqpdist from the bioinformatics toolbox to calculate distance matricies for DNA alignments downloaded from ensembl. These alignments may include N's (for ambiguous data), dots for no sequence data, and dashes for gaps.

Does seqpdist recognize these notations for missing data (N and dots) and gaps (dashes) by default, or are there arguments to set this?

Thanks for your help



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