### `Added`

- Added the `cmaple` module for optional phylogenetic tree inference for final family full MSAs.

### `Changed`

- Updated metro-maps, citations, README.md and output.md to include `cmaple` phylogenetic trees.

### `Fixed`

- Fixed a bug in `REMOVE_REDUNDANCY` subworkflow, where the combination of these skip flags `--skip_sequence_redundancy_removal true`, `--skip_additional_sequence_recruiting true` and `--skip_additional_sequence_recruiting false`, would execute `HHSUITE_REFORMAT_FILTERED` to reformat Stockholm alignments while they were already in fasta (or clipkit) format.