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Name: phybin
Version: 0.3
License: BSD3
License-file: LICENSE
Stability: Beta
Author: Ryan Newton <rrnewton@gmail.com>
Maintainer: Ryan Newton <rrnewton@gmail.com>
-- Version history:
-- 0.1.2 -- first significant release
-- 0.1.2.1 --
-- 0.1.2.4 -- new release, several new features
-- 0.1.2.5 -- bump for graphviz API changes
-- 0.2 -- Add Robinson-Foulds distance, use Int labels.
-- 0.2.2 -- misc changes and expose library
-- 0.2.4 -- add consensus trees
-- 0.2.6 -- colorization, hashrf, misc improvements
-- 0.2.7 -- Add command line opt --showtrees
-- 0.2.8 -- Add command line opt --highlight
-- 0.2.9 -- Add command line opt --interior
-- 0.2.10 -- Add command line opt --matching
-- 0.2.11 -- Cleanup and windows compatibility.
-- 0.3 -- significant improvements and new functionality.
-- homepage: http://code.haskell.org/phybin
-- homepage: http://people.csail.mit.edu/newton/phybin/
homepage: http://www.cs.indiana.edu/~rrnewton/projects/phybin/
Copyright: Copyright (c) 2010 Ryan Newton
Synopsis: Utility for clustering phylogenetic trees in Newick format based on Robinson-Foulds distance.
Description:
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).
Category: Bioinformatics
Cabal-Version: >= 1.8
Extra-source-files: README.md
Build-type: Simple
Source-repository head
type: git
location: git://github.com/rrnewton/PhyBin.git
Flag hashrf
description: Use the HashRF algorithm by default instead of the naive one.
default: True
Flag bitvec
description: Use bitvectors rather than IntSets for bipartitions.
default: False
Flag sequential
description: Don't use any parallelism at all.
default: False
Library
Exposed-modules: Bio.Phylogeny.PhyBin
Bio.Phylogeny.PhyBin.Binning
Bio.Phylogeny.PhyBin.CoreTypes
Bio.Phylogeny.PhyBin.Parser
Bio.Phylogeny.PhyBin.PreProcessor
Bio.Phylogeny.PhyBin.RFDistance
Bio.Phylogeny.PhyBin.Util
Bio.Phylogeny.PhyBin.Visualize
-- Data.BitList
Build-Depends: base >= 3 && < 5, directory, process, containers,
async, time,
filepath,
graphviz >= 2999.16,
text,
prettyclass, fgl,
HUnit, bytestring,
-- For bytestring.lazy support:
parsec >= 3.1.0,
vector >= 0.10,
hierarchical-clustering >= 0.4, split >= 0.2
-- lattice-par,
GHC-Options: -O2 -funbox-strict-fields -rtsopts
if flag(hashrf)
CPP-Options: -DUSE_HASHRF
if flag(bitvec)
CPP-Options: -DBITVEC_BIPS
Build-Depends: bitvec >= 0.1
if flag(sequential)
CPP-Options: -DSEQUENTIALIZE
Executable phybin
Main-is: Main.hs
Build-Depends: phybin
-- DUPLICATE:
Build-Depends: base >= 3 && < 5, directory, process, containers,
async, time,
filepath,
graphviz >= 2999.16,
text,
prettyclass, fgl,
HUnit, bytestring,
-- For bytestring.lazy support:
parsec >= 3.1.0,
vector >= 0.10,
hierarchical-clustering >= 0.4, split >= 0.2
-- lattice-par,
GHC-Options: -O2 -funbox-strict-fields -rtsopts -threaded
if flag(hashrf)
CPP-Options: -DUSE_HASHRF
if flag(bitvec)
CPP-Options: -DBITVEC_BIPS
Build-Depends: bitvec >= 0.1
if flag(sequential)
CPP-Options: -DSEQUENTIALIZE
-- DUPLICATED from executable:
Test-Suite test-phybin
Main-is: TestAll.hs
Type: exitcode-stdio-1.0
-- Build-Depends: phybin
Build-Depends: base >= 3 && < 5, directory, process, containers,
async, time,
filepath,
graphviz >= 2999.16,
text,
prettyclass, fgl,
HUnit, bytestring,
parsec >= 3.1.0,
vector >= 0.10,
hierarchical-clustering >= 0.4, split >= 0.2
-- Additional depends for test:
Build-Depends: HUnit, test-framework, test-framework-hunit, test-framework-th
GHC-Options: -O2 -funbox-strict-fields -rtsopts -threaded
if flag(hashrf)
CPP-Options: -DUSE_HASHRF
if flag(bitvec)
CPP-Options: -DBITVEC_BIPS
Build-Depends: bitvec >= 0.1
if flag(sequential)
CPP-Options: -DSEQUENTIALIZE
|
