Informed paralog filtering removes my outgroup

[DavCP]

Hello again.

While processing some samples, I noticed something strange: despite my outgroup sample having almost no paralogs, a high proportion of loci in the informed directory have my outgroup removed. Is there a reason for this? I thought paralog filtering was only supposed to filter out copies.

I'd really appreciate some insight, maybe I've misunderstood something.

[DavCP]

Well, I seem to have found the reason while trying to get my head around the documentation. The default --tolerance is deleting some of my samples. At least for my dataset It's best to disable that filtering.

I'm not sure if it would be beneficial to include a warning in the documentation stating that the informed filtering can remove sequences even when there are no copies or paralogs.