... markup_to_file did not actually work until now, rather it removed all gaps from alignment . ... 3 This release collects a lot of changes that happened during half year . ... 12 * and a lot of work on ` blocks3d ` and ` pair_cores ` with many new features , . ... 23 * new ( ! ... 51 * change : new method blocks_from_homology () . ... 68 * new : Alignments , Sequences and Blocks now can have Markups , see the wiki . 69 * new : File format 'markup' for storing alignment with arbitrary markups . ...