ALICAO is a program to perform contact-based sequence alignment, where the structure of the first sequence is known (template) and the sequence of the second sequence is unknown (query). A contact map is extracted from the template structure and the program aligns the two sequences by maximizing a combination of contact mutation and sequence mutation probability. The combination of structure and sequence information overall improves alignments between sequences with < 30% sequence identity.
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J. Kleinjung, J. Romein, K. Lin and J. Heringa,
Contact-based sequence alignment,
Nucleic Acids Research 32(8) (2004) 2464-2473