0.3 (Nov 2021--May 2022)
- Implement efficient affine gap cost alignment
with O(n^2 max_shift^2) time complexity, 9 states and 15 cases per state - Preserve implementation of non-affine algorithm
(it is automatically chosen for gap_opening_cost 0) - Use sparse DP matrix O(n^2 max_shift^2)
- Support similarity matrix for protein comparison, include BLOSUM62
- Rewrite code for compilation with Cython and optimize due to static typing
- Support input from files
- Graphic representation of protein alignments
- Smart trace back preferring more natural shifts (in case of
ambiguity) - add pip and conda packaging
- cleanup
- improve visualization: add shift lines
- improve/update documentation
- minor fixes