Hi. first of all, thank you for this nice package.
My question is that “Is it possible to select the sequences having coverage (=PairwiseAlignmentLength) over certain level from aligned sequences?”
I found that xxx.align.report have such data of PairwiseAlignmentLength.
However, it would be convienient that align() command has an option to set the coverage criterion like the option “threshold=0.75”.
When I aligned some sequences having contaminant sequences, in some contaminated sequences, even 10% of sequences were not aligned with db sequences, (it means that they have low coverage (=PairwiseAlignmentLength)) but we cannot descriminate them with other sequences aligned well without coverage threshold level because they often have high similarity value.
If there is possible way to perform it now, let me know it or it can be an option for next improvement of the mothur package.