@hackage phybin0.2.2

Utility for clustering phylogenetic trees in Newick format based on Robinson-Foulds distance.

% PhyBin: Binning Trees by Topology

PhyBin is a simple command line tool that classifies (bins) a set of Newick tree files by their topology. The purpose of it is to take a large set of tree files and browse through the most common tree topologies.

(Above figure) Trees corresponding to the three largest bins resulting from aphybin run. The file binXX_YYY, where XX is the rank of the bin andYYY is the number of trees having that topology.

Invoking PhyBin

PhyBin is a command-line program that produces output in the form of text files and pdfs, but to produce pdfs (to visualize trees) the GraphViz program, including the dot command, must be installed on the machine.

The following is a typical invocation of PhyBin:

phybin *.tree -o output_dir/

The input trees can be specified directly on the command-line, or, if the name of a directory is provided instead, all contained files are assumed to be trees in Newick format.

PhyBin, at minimum, produces files of the form output_dir/binXX_YY.tr, one for each bin. If requested, it will also produce visual representations of each bin in the form output_dir/binXX_YY.pdf.

Downloading and Installing PhyBin

The source code to PhyBin can be downloaded here:

PhyBin is written in Haskell and if you have Haskell Platform. installed you can install phybin with this one-liner:

cabal install phybin

PhyBin is also available for download as a statically-linked executable for Mac-OS and Linux:

It should be possible to build it for Windows, but I haven't done so yet.

Command-line Options

In addition to input files and directories, phybin supports a number of command-line options. Run "phybin --help" to see these options.

Authors: Irene and Ryan Newton

Contact email: irnewton indiana edu (with "at" and "dot" inserted).

.