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

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

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

Author(s) -

Carolyn J. Lawrence,

Christian M. Zmasek,

R. Kelly Dawe,

Russell L. Malmberg

Publication year - 2004

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bth180

Subject(s) - phylogenetic tree , multiple sequence alignment , tree (set theory) , network topology , computer science , heuristic , inference , sequence alignment , sequence (biology) , r package , alignment free sequence analysis , artificial intelligence , random tree , software , topology (electrical circuits) , mathematics , biology , combinatorics , genetics , peptide sequence , computational science , gene , motion planning , robot , programming language , operating system

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

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