HEALY, JOHN* and NELSON D. YOUNG. Dept.of Biology, Trinity University, 715 Stadium Dr., San Antonio TX 78212. - A new computer program, GapCoder allows inclusion of indels as characters in phylogenetic analysis.
The position of indels (gaps) in molecular data sets can be useful
phylogenetic information, yet this information is rarely used,
especially in large data sets with many indels. We have written a
program that codes indels as characters for phylogenetic analysis.
This program is also useful for exploratory analyses of optimal DNA
sequence alignment. The program, GapCode, parses aligned data sets,
generates indel characters and produces a NEXUS-format output file,
complete with a table of correspondences between the indels and their
codes. We base our algorithm on the "simple gap coding"
method of Simmons, M.P. and H. Ochoterena, 2000. Systematic Biology
49:369-381. In this method, indels are coded as the same if they start
and end in the same place. Instructions on how to obtain a free copy
of the program will be included in the poster.
Key words: gap coding, indel, NEXUS, phylogenetic software, sequence alignment