The multiple alignment procedures implemented in MALIGN are close parallels to those used to search for minimum length cladograms. The logic and program commands will be clear to those familiar with programs such as Hennig86, NONA, and PAUP. Alignment topologies are constructed via different sequence addition sequences and improved through branch swapping. Each alignment topology yields a multiple alignment and cladograms are constructed from that alignment.

The cost of the most parsimonious cladogram is then assigned as the multiple alignment cost. This document describes the underlying concepts and practical usage of MALIGN, a multiple sequence alignment program. Although MALIGN can be used to process amino acid data (by conversion to nucleotide triplets), this program is designed to analyze nucleic acid sequences. Therefore, most of the discussion and examples refer to DNA / RNA data although they pertain to both sequence types.

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