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Old 10-29-2014, 12:11 AM   #2
Location: Scotland

Join Date: Feb 2011
Posts: 29

Generally, you need to compare all strains with all other strains. You only have reciprocal BLAST hits between two strains A and B if the BLAST has been performed reciprocally: A vs B, and B vs A.

That's 40 x 40 - 40 = 1560 comparisons, for 40 strains.

I can imagine circumstances where, if the only differences between a pair of isolates were SNPs, you could make assumptions and avoid the comparison. I'd typically just run the comparison, anyway.
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