I have a very simple question: having used the filter.seqs command with the vertical=true and trump=. options, my sequences end up getting shortened. Does this affect the distance matrix calculations (and the clustering into OTUs based upon it)? They used to be ~400 bp and are now around~250 - i.e. 10 bp difference between two sequences is now 2,5% and 4% difference - unless the identical columns removed by the filter are still somehow counted in the dist.seqs, too.
Are they? And if not, then what should one preferably do? When I filter my sequences and leave out the trump=., step, then pre.cluster takes forever.
Best regards,
Christoffer