Name:           phybin
Version:        0.2.2
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

-- homepage: http://code.haskell.org/phybin
homepage: http://people.csail.mit.edu/newton/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.
   .
   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

Library
  Exposed-modules:   Bio.Phylogeny.PhyBin
                     Bio.Phylogeny.PhyBin.RFDistance
                     Bio.Phylogeny.PhyBin.Parser
                     Bio.Phylogeny.PhyBin.CoreTypes
                     Bio.Phylogeny.PhyBin.Binning
                     Bio.Phylogeny.PhyBin.Util
                     Bio.Phylogeny.PhyBin.Visualize
--  Other-modules:     Data.BitList
  Build-Depends:     base >= 3 && < 5, directory, process, containers, unix, 
                     async, time,
                     filepath, 
                     graphviz >= 2999.16, 
                     text >= 0.11 && < 0.12,
                     prettyclass, fgl,
                     HSH, HUnit, bytestring, 
                     -- For bytestring.lazy support:
                     parsec >= 3.1.0, 
                     bitvec >= 0.1, vector >= 0.10,
                     hierarchical-clustering >= 0.4
--                     lattice-par, 
  GHC-Options: -O2 -funbox-strict-fields -rtsopts

Executable phybin
  Main-is:           Main.hs
  Build-Depends:     phybin
  -- DUPLICATE:
  Build-Depends:     base >= 3 && < 5, directory, process, containers, unix, 
                     async, time,
                     filepath, 
                     graphviz >= 2999.16, 
                     text >= 0.11 && < 0.12,
                     prettyclass, fgl,
                     HSH, HUnit, bytestring, 
                     -- For bytestring.lazy support:
                     parsec >= 3.1.0, 
                     bitvec >= 0.1, vector >= 0.10,
                     hierarchical-clustering >= 0.4
--                     lattice-par, 
  GHC-Options: -O2 -funbox-strict-fields -rtsopts