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

Carolyn J Lawrence; Christian M Zmasek; R Kelly Dawe; Russell L Malmberg

doi:10.1093/bioinformatics/bth180

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

Carolyn J Lawrence·Christian M Zmasek·R Kelly Dawe·Russell L Malmberg

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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, 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

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Algorithms Conserved Sequence Likelihood Functions Phylogeny Sequence Alignment Sequence Analysis, DNA Sequence Homology, Nucleic Acid Software User-Computer Interface Journal Article Research Support, U.S. Gov't, Non-P.H.S.

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Carolyn J Lawrence, Christian M Zmasek, R Kelly Dawe, Russell L Malmberg. 2004-03-25. LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference.. https://doi.org/10.1093/bioinformatics%2Fbth180

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