1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149
|
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
|