Tree Searches under Sankoff Parsimony

Abstract

Algorithms to speed up tree searches under Sankoff parsimony are described. For T terminal taxa, an exact algorithm allows calculating length during searches T to 27 times faster than a complete down-pass optimization. An approximate but accurate method is from 3T to 87 times faster than a down-pass. Other algorithms that provide additional increases of speed for simple symmetrical transformation costs are described. © 1998 The Willi Hennig Society.