The phybin package

[Tags: bsd3, library, program]

This package provides a libary and executable for dealing with Newick tree files.

It can do simple binning of identical trees or more complex clustering based on an all-to-all Robinson-Foulds distance matrix.

phybin produces output files that characterize the size and contents of each bin or cluster (including generating GraphViz-based visual representations of the tree topologies).


Properties

Versions0.1, 0.1.1, 0.1.2, 0.1.2.1, 0.1.2.4, 0.1.2.5, 0.2.2, 0.2.11, 0.3
Dependenciesasync, base (>=3 && <5), bytestring, containers, directory, fgl, filepath, graphviz (>=2999.16), hierarchical-clustering (>=0.4), HUnit, parsec (>=3.1.0), phybin, prettyclass, process, split (>=0.2), text (==0.11.*), time, vector (>=0.10)
LicenseBSD3
CopyrightCopyright (c) 2010 Ryan Newton
AuthorRyan Newton <rrnewton@gmail.com>
MaintainerRyan Newton <rrnewton@gmail.com>
StabilityBeta
CategoryBioinformatics
Home pagehttp://www.cs.indiana.edu/~rrnewton/projects/phybin/
Source repositoryhead: git clone git://github.com/rrnewton/PhyBin.git
Executablesphybin
Upload dateFri Sep 20 11:47:04 UTC 2013
Uploaded byRyanNewton
Downloads413 total (39 in last 30 days)

Modules

Flags

NameDescriptionDefault
hashrfUse the HashRF algorithm by default instead of the naive one.Enabled
bitvecUse bitvectors rather than IntSets for bipartitions.Disabled
sequentialDon't use any parallelism at all.Disabled

Use -f <flag> to enable a flag, or -f -<flag> to disable that flag. More info

Downloads

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