LUMBERJACK: A Heuristic Tool For Sequence Alignment Exploration And Phylogenetic Inference

Carolyn J. Lawrence1, Christian M. Zmasek2, R. Kelly Dawe, Russell L. Malmberg, Department of Plant Biology, University of Georgia Athens;, Genomics Institute of the Novartis Research Foundation

LumberJack is a phylogenetic tool intended to serve two purposes: 1. to facilitate sampling treespace to find likely tree topologies quickly and 2. to map phylogenetic signal onto regions of an alignment in a heuristic manner. LumberJack creates jackknifed alignments by progressively sliding a window of omission along the alignment. A neighbor joining tree is built from the full alignment and from each jackknifed alignment, and the likelihood for each topology (given the original full alignment) is calculated. To determine whether any of the topologies generated is significantly more likely than the others, the Kishino-Hasegawa test is implemented.