Would not using the filter.seqs command have a negative impact on data recovery and analysis? Doesn’t screen.seqs, chimera removal, and alignment solve the purpose of filtering high quality sequences?
No, it doesn’t remove any data. The vertical=T option removes columns that only contain gap characters (no bases) and the trump=. option makes it so that the alignment starts and ends at the same coordinates in the alignment. This second point is critical to make sure you’re not comparing sequences that span different regions/bases.
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