C implementation of Local and Global alignment using classic dinamic programming algorithms
In order to try the library out you can run the makefile and try out (minimun a file for d and q sequences):
#To try Global alignment: ./Main global data/affine1d.fasta data/affine1q.fasta data/affine2d.fasta data/affine2q.fasta
#To try local alignment ./Main local data/local1d.fasta data/local1q.fasta data/local2d.fasta data/local2q.fasta data/local3d.fasta data/local3q.fasta data/local5d.fasta data/local5q.fasta
The format of input files is the following, specify if you want query or database sequence (>q or >d respectively) and under it the sequence you want.
q ACCT
You can also change the scoring system for global and local alignment at their corresponding .h files