PSSAT - Protein Secondary Structure Alignment Tool help you align two proteins, using secondary structure output predicted by PSIPRED. Developed in Haskell, using wxHaskell for GUI.
This tool will create a visual global or local alignment of two proteins, using the following novel techniques:
1. Uses confidence intervals returned by PSIPRED to determine match scores
2. Affine gap penalty - alignments prefer long, continuous gaps over many short gaps
3. Includes original amino acid sequence for reference
4. Output in HTML format to aid in visualization, or as plain text

The license of this software is Free, you can free download and free use this calculator software.