Original published version

• Position Specific Subsititution Matrices (PSSMs) supported as an alignment input
• ClustalW and Fasta-Format output of the aligned sequences supported
• extraction of two sequences from the alignment of two averaged MSAs possible
• gaps are now "?0" in the profiles - no more confusion of gaps with profile values having a 0
• added a perl script with the best parameters for alpha-helical proteins to run in "PST" mode
• improved error feedback
• version used for PLoS One manuscript

Initial release

Sequence and profile alignments using Needleman Wunsch algorithm