Alignment Resources

There are a number of alignment programs available for use through SACS web interfaces.

These programs are open to the general public. The user supplies a fasta file for their sequences of interest and the selected program then generates an alignment.

There are four pairwise alignment programs: needle and stretcher which preform global alignments plus matcher and water which preform local alignments.

Multiple alignments are handled by clustalw, multalin, muscle and t_coffee. The multalin and t_coffee programs produces colored images of their alignments. Clustalw, multalin and t_coffee produce files that can be used in the drawgram or drawtree interfaces.

The image at the left is from a t_coffee run.