MEDIAN STRING [Fast Median String Finding Algorithm]


MEDIAN STRING:
-------------
Finds the median string of required length (input) from the given set of sequences in FASTA format. It uses a new Branch and Bound algorithm which prunes the subtrees more faster than ordinary Branch and Bound algorithm.
** This algorithm is an implementation of work which is still unpublished.
USAGE:
-----
mediansting < input.txt
input.txt is a FASTA file except the first line is the length of the median string you are searching in the fasta sequences.
1. make clean
1.1 make depend
2. make

DOWNLOAD:
--------
MedianString-1.0

CENTER STAR [Multiple String Alignment]


CENTER STAR Algorithm:
----------------------
Its been a well know fact that the problem of Multiple Sequence Alignment is NP-Complete, CENTER STAR Algorithm is an approximation algorithm which has a constant approximation ratio 2 with the optimal alignment. This program implements the CENTER STAR algorithm for Multiple Sequence Alignment(MSA) problem, the program computes the score of the alignment and also prints the acutal alignment.
USAGE:
------
1. make
2. ./malign < input.txt
input.txt is a text file as follows
[integer indicating # of strings] [string1]
[string2]
Example:
-------- 
input.txt
------
5
abcdddddef
acdddd
aef
abef
ddddddd
-------
$ ./malign < test_input.txt 
best star cost: 17
total cost: 60
abcdddddef
a-cdddd---
a-------ef
a------bef
---ddddddd
Download the code here