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


BACKGROUND
http://www.plantbio.uga.edu/~russell/software.html
Lawrence
Carolyn J
CJ
Department of Plant Biology, The University of Georgia, Athens 30602, USA.
Zmasek
Christian M
CM
Dawe
R Kelly
RK
Malmberg
Russell L
RL
D000465:Algorithms; D017124:Conserved Sequence; D016013:Likelihood Functions; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D014584:User-Computer Interface