Key points are not available for this paper at this time.
In the analysis of sequence-based data matrices, the use of different methods of treating gaps has been demonstrated to in? fluence the resulting phylogenetic hypothe? ses (e.g., Eernisse and Kluge, 1993; Vogler and DeSalle, 1994; Simons and Mayden, 1997). Despite this influence, a well-justi? fied, uniformly applied method of treating gaps is lacking in sequence-based phyloge? netic studies. Treatment of gaps varies widely from secondarily mapping gaps onto the tree inferred from base characters
Simmons et al. (Thu,) studied this question.