YOUNG, NELSON D.* and JOHN HEALY. Dept. of Biology, Trinity University, 715 Stadium Dr., San Antonio TX 78212. - Incorporating indels as characters in phylogeny and the search for the best multiple sequence alignment.
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