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
UploadedFri Sep 20 11:47:04 UTC 2013 by RyanNewton
Downloads832 total (51 in last 30 days)
StatusDocs uploaded by user
Build status unknown [no reports yet]

Modules

[Index]

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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