Tool for removing bad quality sequences from MSA

Question

[GR]

Hello everyone,

I am looking for a tool that can remove bad quality sequences from MSA. I used trimal (with option -resoverlap 0.6 -seqoverlap 50) but it removes the bad quality colums as well, which I don't want (let me know if trimal already does that and I am missing the correct option).

If anyone knows a tool that can quickly report/remove the bad quality sequences then it would be very much helpful. Standalone tool will be useful.

Thanks

Answer 1

[HA]

I don't know if trimal can remove only bad quality sequences from the MSA but GUIDANCE can point out such sequences.

Note that after you remove the bad sequence, the wise thing to do is probably to re-align the sequences left.