One limitation to exploratory analyses of optimal DNA sequence alignment has been the lack of a computer program to code indels (gaps) as characters for phylogenetic analysis. We have produced a program, GapCoder, which does this. It can be used as part of an objective method to find the best multiple sequence alignment. The method involves four stages; (1) producing several alignments, either by eye or by using a program such as Clustal X. (2) coding indels as additional characters in the data matrix, using GapCoder. (3) doing a phylogenetic analysis based on each of the alignments, using PAUP or other phylogeny software. (4) choosing the best alignment according to the optimality-criterion, such as the following; the best alignment is the one that produces phylogenies with the least homoplasy. Examples from ITS and matK will be used to illustrate the method. Instructions on how to obtain a free copy of the program will be given during the talk.

Key words: gap coding, ITS, matK, Orobanchaceae, phylogenetic software, sequence alignment