Lumberjack

A Heuristic Tool for Sequence Alignment Exploration and Phylogenetic Inference

Carolyn J. Lawrence, Christian M. Zmasek, R. Kelly Dawe, and Russell L. Malmberg

PubMed Bioinformatics

ABSTRACT

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.

Click here to download the 7.10 version.

It's been tested on UNIX only so far, and compiles fine on Linux RedHat 8.0 and 9.0 and on MacOS X with the developer tools installed.

Here are some hints:
Execute "gunzip LumberJack.tar.gz" to unzip the file.
Execute "tar -xvf LumberJack.tar" to get the files out of the archive.

To compile and install on your machine:
In directory "LumberJack7.10" execute "javac LJ/LumberJack.java"
In directory "LumberJack7.10/LJ/puzzle_mod" execute "./configure"
In directory "LumberJack7.10/LJ/puzzle_mod" execute "make"

To run LumberJack interactively:
In directory "LumberJack7.10" execute "java LJ.LumberJack"

To run LumberJack at the command line:
In directory "LumberJack7.10" execute "java LJ.LumberJack [input alignment file] [window size] [window overlap] [model] [output file name]"
(e.g., execute "java LJ.LumberJack prot_test_alignment.phy 100 0 VT vtoutput")

The test infiles can be found at /LumberJack/dna_test_alignment.phy and /LumberJack/prot_test_alignment.phy

Please don't email me with bugs. It's only an alpha version so I'm aware of lots of them already. I'll be more amenable to suggestions a little later... It's been tested on UNIX only so far, and compiles fine on Linux RedHat 8.0 and 9.0 and on MacOS X with the developer tools installed.