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Essential algorithms for sequence alignment - in Python

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Name		Name	Last commit message	Last commit date
Latest commit History 28 Commits
LICENSE		LICENSE
README		README
function_testing_module.py		function_testing_module.py
other_functions.py		other_functions.py
sequence_alignment.py		sequence_alignment.py

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Essential algorithms for sequence alignment
Author: Aggelos Pikrakis, Eng., Ph.D.
email: [email protected]
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--- Distributed under the GNU General Public License v2.0

This package contains Python implementations of the following sequence alignment algorithms:

(1) Edit distance: edit_distance(y,x)
(2) Dynamic Time Warping using the Sakoe-Chiba constraints: dtw_distance_sc(y,x)
(3) Dynamic Time Warping using the Itakura constraints: dtw_distance_sc(y,x)
(4) Longest Common Subsequence algorithm: lcs(y,x)

- In all cases, y is the test pattern and x is the reference pattern. 
- All current implementations refer to 1-dimensional sequences. 
- Due to the symmetric nature of some constraints, e.g., (2), it is sometimes unimportant which template is placed on which 
axis (this does not always hold). Please read the literature for a theoretical study of the implemented algorithms 
(references will be added as the project develops).
- For reporting bugs, please use github's infrastructure. For questions, please use the email above.

Best wishes,

Aggelos Pikrakis