_**Added a new feature:**_ Insertions can now be aligned by a third party aligner with the optional flag `--align_insertions.` This improves performance when rare, but relevant insertions with respect to the main model occur. Previously, potentially long sequence segments were left unaligned by learnMSA alone.
We currently support famsa (default choice), clustalo and t_coffee (regressive version is used). Either one must be installed separately and visible to learnMSA. We plan to intergrate at least one default aligner in the installation in the future.