Python implementation of the Smith-Watermann algorithm for the course Algorithms for bioinformatics, held by prof. Blanzieri and prof. Tebaldi.
The script will ask the user to input two sequences. In case of no specification of the other parameters, the default parameters will be used.
The basic output given two sequences (e.g., AAACGCT and AATCCG), will look like this:
RESULTS:
Score: 8 Match score: 3 Gap penalty: 2
SEQUENCE: AA+C-C
Score: 8 Match score: 3 Gap penalty: 2
SEQUENCE: AA+C+G
SEQUENCE: AA++CG
Where score is the score of the alignment. If two (or more) sequences are not separated by the score line (in this example, Score: 8 Match score: 3 Gap penalty: gap), it means that the sequences were reconstructued during the backtrack starting from the same initial cell.
By running the script with the -l option, a longer output containing other statistics will be printed.
Mismatches will be denoted with an "X".
The options for the script will be displayed by running the script with -h, or can be found in the help.txt file.