https://github.com/dcasella/carrillo-lipman
Carrillo-Lipman algorithm implementation
https://github.com/dcasella/carrillo-lipman
bioinformatics c msa
Last synced: over 1 year ago
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Carrillo-Lipman algorithm implementation
- Host: GitHub
- URL: https://github.com/dcasella/carrillo-lipman
- Owner: dcasella
- Created: 2016-12-31T19:25:25.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2017-03-14T10:09:59.000Z (over 9 years ago)
- Last Synced: 2025-03-26T02:51:25.702Z (over 1 year ago)
- Topics: bioinformatics, c, msa
- Language: C
- Homepage:
- Size: 1.95 KB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Carrillo Lipman
> Algorithm explained in section 14.6.1 "A speedup for the exact solution" from Dan Gusfield's "Algorithms on Strings, Trees, and Sequences"
Implementation of the Carrillo-Lipman algorithm for aligning three sequences.
This is an heuristic of the multiple sequence alignment problem with the Sum-of-Pairs objective function.
The algorithm takes in input three strings and a parameter *upper_bound*, and prints the score of the best possible alignment between the strings.
## Interface
```c
void multi_align(char *seq_a, char *seq_b, char *seq_c, size_t upper_bound);
```
## Example
```c
size_t upper_bound = 42;
multi_align("seq1", "seq2", "seq3", upper_bound);
```