Before the beginning, I recommend you to know some basic of pairwise alignment algorithms such as Needleman-Wunch algorithm because I use to calculate pairwise alignments by Needleman-Wunch.

1. Find Sc maximizing Σic D(Sc, Si ).(Note: Some resources say minimizing)
2. Iteratively construct the multiple alignment Mc:
   1. Mc={Sc}
   2. Add the sequences in S{Sc} to Mc one by one so that the induced alignment aMc(Sc, Si) of every newly added sequence Si with Sc is optimal. Add spaces, when needed, to all pre-aligned sequences.

Combination(k,2) * O(n^2) = O(k^2 * n^2)

AC-BC
DCABC

AC--BC
DCAABC

=

AC--BC
DCA-BC
DCAABC

The format of the input file must be this way;

{matchScore},{mismatchScore},{gapScore}
{sequence1}
{sequence2}
{sequence3}
.
.
.
{sequenceN}

for example; whether matchScore = 1, mismatchScore = -1, gapScore = -4 and four strings, the file should be;

1,-1,-4
MPE
MKE
MSKE
SKE

python cstar.py inputfile outputfile

• Score matrix support []