Bioinformatics Advance Access originally published online on March 25, 2004
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Bioinformatics 20(12) © Oxford University Press 2004; all rights reserved.
Applications Note |
LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference
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1 Department of Plant Biology and 2 Department of Genetics, The University of Georgia, Athens, GA 30602, USA and 3 Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
Received on August 7, 2003; revised on March 3, 2004; accepted on March 4, 2004
Advance Access Publication March 25, 2004
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, and 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
Contact: russell{at}plantbio.uga.edu
* To whom correspondence should be addressed.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
Present address: Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.