CIAlign vs HmmCleaner, PREQUAL, and spruceup

[fdecarpentier]

Hi Katy,

Thank you for CIAlign, it looks like an amazing and unique tool. First of all, I'm no expert by any means so please lmk if I got something wrong.
In the paper, you compare it with trimming tools such as trimAl, i.e. column-based algorithms. However, some CIAlign features fall more in the msa filtering category.
So, would you be able to compare/benchmark CIAlign with other filtering tools :

• PREQUAL : https://doi.org/10.1093/bioinformatics/bty448
• HmmCleaner : https://doi.org/10.1186/s12862-019-1350-2
• spruceup : https://doi.org/10.21105/joss.01635

Cheers!