I 'm looking for a smith.waterman implementation that given two sequences (and all respective parameters like match, mismatch/gap penalty and so) returns me the list of alignments and the begining and end in both sequences.
Implementations that do not do what we need:
- Biopython pairwise2 does not return that
- This c library neither ttps://github.com/mengyao/Complete-Striped-Smith-Waterman-Library
- python's swalign https://pypi.python.org/pypi/swalign
Preferably should be a C library we can port into python, but given the things we found I don't think we are going to be so lucky.