Option to disallow gap and/or N and/or non-AGTC ?

[tseemann]

We are impressed by the speed of this tool (due to being C code).

A very useful feature we need to the ability to also filter out things like:

• gap -
• N
• non-AGTC eg * and X etc

These would need to be independent options.

Ideally the current default behaviour to remove conserved (monmorphic) sites could also be an option. eg. so we could remove all columns with a gap only and leave the rest.

[ONeillMB1]

Great tool! We also are very impressed with the speed!

Building off the recommendation of @tseemann, it would also be nice to be able to impose thresholds for tolerable amounts of missing data. For example, if 75% of samples in the alignment have data and there exists a SNP among them, retain the data in the SNP alignment.

[andrewjpage]

I've added in a 'pure' mode as discussed with @tseemann and a 'keep monomorphic' mode (so it will work with BEAST).

[jamiethompson77]

This does work with amino acids though right?

[tseemann]

@jamiethompson77 i think AGTC is quite hard-coded into the tool, sorry. snp is in the name and that is DNA specific.