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Bioinformatics Advance Access published online on March 25, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth180
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received August 7, 2003
Revised March 3, 2004
Accepted March 4, 2004

Applications note

LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference

Carolyn J. Lawrence 1, Christian M. Zmasek 2, R. Kelly Dawe 3, Russell L. Malmberg 1*

1 Department of Plant Biology, The University of Georgia, Athens, GA 30602
2 Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121
3 Department of Plant Biology, The University of Georgia, Athens, GA 30602; Department of Genetics, The University of Georgia, Athens, GA 30602

* To whom correspondence should be addressed. E-mail: russell{at}plantbio.uga.edu.


  Abstract

Summary: LumberJack is a phylogenetic tool intended to serve two purposes: to facilitate sampling treespace to find likely tree topologies quickly and to map phylogenetic signal onto regions of an alignment in a revealing way. LumberJack creates non-random 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, then 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, Kishino-Hasegawa, Shimodaira-Hasegawa, and ELW tests are implemented.

Availability and Supplementary Information: http://www.plantbio.uga.edu/~russell/software.html.


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