Removal of hypervariable sequences

[BenKuhnhaeuser]

Hi there, I love how the phyx family is expanding to include so many useful capabilities. I would like to suggest a program that removes highly divergent / hypervariable sequences from multiple sequence alignments. Such highly divergent sequences can point to various issues, such as chimeric or paralogous sequences being mixed up in an alignment. The tool would calculate the number of sites divergent from the consensus sequence (similar to calculating missing sites), and remove sequences above the specified threshold.

A "sliding window" option would be even cooler to clean short stretches of highly divergent sequences in otherwise perfectly aligned and well-behaved sequences without discarding the entire sequence.

Many thanks for the consideration! Ben