Release Notes for AlignMe

Version 1.2

• Inclusion of anchors as constraints
• Pairwise alignments can be performed in a batch mode (relevant for the server)

Version 1.1

• 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 the package
• Improved error feedback

Version 1.0

Initial release