Readme for phybin-0.2.11
% 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.
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).
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