Sequence alignment learning materials

sequence alignment implementation with python

Pairwise Sequence Alignment

1. Dynamic programming with linear gap penalty

   code

2. Dynamic programming with affine gap penalty

   code

3. k-band Dynamic programming with affine gap penalty

   code

4. k-band Dynamic programming with affine gap penalty (memory saving)

   code

5. Divide-Conquer strategy (memory saving)

   code

6. PSA with suffix tree (use in MACF)

   code

7. PSA with FM-index (use in MACF)

   code

Multiple Sequence Alignment

1. center star alignment

   code

2. center star alignment (multi-cores)

   code

License

This repo is released under the MIT license. See the file LICENSE for more details.

Contact

If you have any problems, please email me.(ttscj12@gmail.com or 1350854808@qq.com)