libbpp-phyl-dev_2.1.0-1_amd64.deb


Advertisement

Description

libbpp-phyl-dev - Bio++ Phylogenetic library development files

Property Value
Distribution Debian 8 (Jessie)
Repository Debian Main amd64
Package name libbpp-phyl-dev
Package version 2.1.0
Package release 1
Package architecture amd64
Package type deb
Installed size 31.15 KB
Download size 5.51 MB
Official Mirror ftp.br.debian.org
Contains the Bio++ classes for phylogenetics.

Alternatives

Package Version Architecture Repository
libbpp-phyl-dev_2.1.0-1_i386.deb 2.1.0 i386 Debian Main
libbpp-phyl-dev - - -

Requires

Name Value
libbpp-phyl9 = 2.1.0-1
libbpp-seq-dev >= 2.1.0

Download

Type URL
Binary Package libbpp-phyl-dev_2.1.0-1_amd64.deb
Source Package libbpp-phyl

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install libbpp-phyl-dev deb package:
    # sudo apt-get install libbpp-phyl-dev

Files

Path
/usr/include/Bpp/Phyl/AncestralStateReconstruction.h
/usr/include/Bpp/Phyl/BipartitionList.h
/usr/include/Bpp/Phyl/BipartitionTools.h
/usr/include/Bpp/Phyl/NNISearchable.h
/usr/include/Bpp/Phyl/NNITopologySearch.h
/usr/include/Bpp/Phyl/Node.h
/usr/include/Bpp/Phyl/NodeTemplate.h
/usr/include/Bpp/Phyl/OptimizationTools.h
/usr/include/Bpp/Phyl/PatternTools.h
/usr/include/Bpp/Phyl/PhyloStatistics.h
/usr/include/Bpp/Phyl/SitePatterns.h
/usr/include/Bpp/Phyl/TopologySearch.h
/usr/include/Bpp/Phyl/Tree.h
/usr/include/Bpp/Phyl/TreeExceptions.h
/usr/include/Bpp/Phyl/TreeTemplate.h
/usr/include/Bpp/Phyl/TreeTemplateTools.h
/usr/include/Bpp/Phyl/TreeTools.h
/usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h
/usr/include/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h
/usr/include/Bpp/Phyl/Distance/BioNJ.h
/usr/include/Bpp/Phyl/Distance/DistanceEstimation.h
/usr/include/Bpp/Phyl/Distance/DistanceMethod.h
/usr/include/Bpp/Phyl/Distance/HierarchicalClustering.h
/usr/include/Bpp/Phyl/Distance/NeighborJoining.h
/usr/include/Bpp/Phyl/Distance/PGMA.h
/usr/include/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h
/usr/include/Bpp/Phyl/Graphics/AbstractTreeDrawing.h
/usr/include/Bpp/Phyl/Graphics/CladogramPlot.h
/usr/include/Bpp/Phyl/Graphics/PhylogramPlot.h
/usr/include/Bpp/Phyl/Graphics/TreeDrawing.h
/usr/include/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h
/usr/include/Bpp/Phyl/Graphics/TreeDrawingListener.h
/usr/include/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h
/usr/include/Bpp/Phyl/Io/BppORateDistributionFormat.h
/usr/include/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h
/usr/include/Bpp/Phyl/Io/IoDistanceMatrix.h
/usr/include/Bpp/Phyl/Io/IoDistanceMatrixFactory.h
/usr/include/Bpp/Phyl/Io/IoFrequenciesSet.h
/usr/include/Bpp/Phyl/Io/IoFrequenciesSetFactory.h
/usr/include/Bpp/Phyl/Io/IoPairedSiteLikelihoods.h
/usr/include/Bpp/Phyl/Io/IoSubstitutionModel.h
/usr/include/Bpp/Phyl/Io/IoSubstitutionModelFactory.h
/usr/include/Bpp/Phyl/Io/IoTree.h
/usr/include/Bpp/Phyl/Io/IoTreeFactory.h
/usr/include/Bpp/Phyl/Io/Newick.h
/usr/include/Bpp/Phyl/Io/NexusIoTree.h
/usr/include/Bpp/Phyl/Io/Nhx.h
/usr/include/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h
/usr/include/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h
/usr/include/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h
/usr/include/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h
/usr/include/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/DRTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h
/usr/include/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h
/usr/include/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h
/usr/include/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h
/usr/include/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.h
/usr/include/Bpp/Phyl/Likelihood/RASTools.h
/usr/include/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/SitePartitionTreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/TreeLikelihood.h
/usr/include/Bpp/Phyl/Likelihood/TreeLikelihoodData.h
/usr/include/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h
/usr/include/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h
/usr/include/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h
/usr/include/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h
/usr/include/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h
/usr/include/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h
/usr/include/Bpp/Phyl/Mapping/SubstitutionCount.h
/usr/include/Bpp/Phyl/Mapping/SubstitutionMapping.h
/usr/include/Bpp/Phyl/Mapping/SubstitutionMappingTools.h
/usr/include/Bpp/Phyl/Mapping/SubstitutionRegister.h
/usr/include/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h
/usr/include/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h
/usr/include/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/AbstractSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/BinarySubstitutionModel.h
/usr/include/Bpp/Phyl/Model/G2001.h
/usr/include/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/MixedSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/MixedSubstitutionModelSet.h
/usr/include/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h
/usr/include/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h
/usr/include/Bpp/Phyl/Model/RE08.h
/usr/include/Bpp/Phyl/Model/RateDistributionFactory.h
/usr/include/Bpp/Phyl/Model/StateMap.h
/usr/include/Bpp/Phyl/Model/SubstitutionModel.h
/usr/include/Bpp/Phyl/Model/SubstitutionModelFactory.h
/usr/include/Bpp/Phyl/Model/SubstitutionModelSet.h
/usr/include/Bpp/Phyl/Model/SubstitutionModelSetTools.h
/usr/include/Bpp/Phyl/Model/TS98.h
/usr/include/Bpp/Phyl/Model/WordSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/Codon/CodonDistanceFitnessPhaseFrequenciesSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/Codon/GY94.h
/usr/include/Bpp/Phyl/Model/Codon/MG94.h
/usr/include/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/Codon/YN98.h
/usr/include/Bpp/Phyl/Model/Codon/YNGKP_M1.h
/usr/include/Bpp/Phyl/Model/Codon/YNGKP_M2.h
/usr/include/Bpp/Phyl/Model/Codon/YNGKP_M3.h
/usr/include/Bpp/Phyl/Model/Codon/YNGKP_M7.h
/usr/include/Bpp/Phyl/Model/Codon/YNGKP_M8.h
/usr/include/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h
/usr/include/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h
/usr/include/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h
/usr/include/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.h
/usr/include/Bpp/Phyl/Model/FrequenciesSet/ProteinFrequenciesSet.h
/usr/include/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h
/usr/include/Bpp/Phyl/Model/Nucleotide/F84.h
/usr/include/Bpp/Phyl/Model/Nucleotide/GTR.h
/usr/include/Bpp/Phyl/Model/Nucleotide/HKY85.h
/usr/include/Bpp/Phyl/Model/Nucleotide/JCnuc.h
/usr/include/Bpp/Phyl/Model/Nucleotide/K80.h
/usr/include/Bpp/Phyl/Model/Nucleotide/L95.h
/usr/include/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/Nucleotide/RN95.h
/usr/include/Bpp/Phyl/Model/Nucleotide/RN95s.h
/usr/include/Bpp/Phyl/Model/Nucleotide/SSR.h
/usr/include/Bpp/Phyl/Model/Nucleotide/T92.h
/usr/include/Bpp/Phyl/Model/Nucleotide/TN93.h
/usr/include/Bpp/Phyl/Model/Nucleotide/YpR.h
/usr/include/Bpp/Phyl/Model/Nucleotide/gBGC.h
/usr/include/Bpp/Phyl/Model/Protein/Coala.h
/usr/include/Bpp/Phyl/Model/Protein/CoalaCore.h
/usr/include/Bpp/Phyl/Model/Protein/DSO78.h
/usr/include/Bpp/Phyl/Model/Protein/JCprot.h
/usr/include/Bpp/Phyl/Model/Protein/JTT92.h
/usr/include/Bpp/Phyl/Model/Protein/LG08.h
/usr/include/Bpp/Phyl/Model/Protein/LGL08_CAT.h
/usr/include/Bpp/Phyl/Model/Protein/LLG08_EHO.h
/usr/include/Bpp/Phyl/Model/Protein/LLG08_EX2.h
/usr/include/Bpp/Phyl/Model/Protein/LLG08_EX3.h
/usr/include/Bpp/Phyl/Model/Protein/LLG08_UL2.h
/usr/include/Bpp/Phyl/Model/Protein/LLG08_UL3.h
/usr/include/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.h
/usr/include/Bpp/Phyl/Model/Protein/WAG01.h
/usr/include/Bpp/Phyl/Model/RateDistribution/ConstantRateDistribution.h
/usr/include/Bpp/Phyl/Model/RateDistribution/ExponentialDiscreteRateDistribution.h
/usr/include/Bpp/Phyl/Model/RateDistribution/GammaDiscreteRateDistribution.h
/usr/include/Bpp/Phyl/Model/RateDistribution/GaussianDiscreteRateDistribution.h
/usr/include/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h
/usr/include/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h
/usr/include/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h
/usr/include/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h
/usr/include/Bpp/Phyl/Parsimony/TreeParsimonyData.h
/usr/include/Bpp/Phyl/Parsimony/TreeParsimonyScore.h
/usr/include/Bpp/Phyl/Simulation/DetailedSiteSimulator.h
/usr/include/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h
/usr/include/Bpp/Phyl/Simulation/MutationProcess.h
/usr/include/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h
/usr/include/Bpp/Phyl/Simulation/SequenceSimulationTools.h
/usr/include/Bpp/Phyl/Simulation/SequenceSimulator.h
/usr/include/Bpp/Phyl/Simulation/SiteSimulator.h
/usr/lib/libbpp-phyl.a
/usr/lib/libbpp-phyl.so
/usr/share/doc/libbpp-phyl-dev/changelog.Debian.gz
/usr/share/doc/libbpp-phyl-dev/changelog.gz
/usr/share/doc/libbpp-phyl-dev/copyright

Changelog

2013-03-07 - Julien Dutheil <julien.dutheil@univ-montp2.fr>
libbpp-phyl (2.1.0-1) unstable; urgency=low
* New RateDistribution classes
* New models for protein sequences (COaLA)
* Support for gaps in parsimony score
* Improved and extended support for BppO
* Several bugs fixed and warnings removed
2013-02-09 - Julien Dutheil <julien.dutheil@univ-montp2.fr>
libbpp-phyl (2.0.3-1) unstable; urgency=low
* Reorganized model hierarchy
* New pairwise models
* Several bugs fixed
2011-06-09 - Julien Dutheil <julien.dutheil@univ-montp2.fr>
libbpp-phyl (2.0.2-1) unstable; urgency=low
* RFP: Bio++ -- The Bio++ bioinformatics libraries. (Closes: #616373).
* Packages are now non-native.
* Exact substitution mapping with detailled counts.
* Backup system for ML estimation.
2011-02-28 - Julien Dutheil <julien.dutheil@univ-montp2.fr>
libbpp-phyl (2.0.1) unstable; urgency=low
* Fixed bug #27
* Improved tree drawing algorithms.
2011-02-07 - Julien Dutheil <julien.dutheil@univ-montp2.fr>
libbpp-phyl (2.0.0) unstable; urgency=low
* Better mixed models
* Extended substitution mapping framework
* More bug fixed, notably in simulation procedures
* Topology comparison tools (ELW)
* Improved graphic classes
2010-03-25 - Julien Dutheil <julien.dutheil@univ-montp2.fr>
libbpp-phyl (1.9.0) unstable; urgency=low
* Several bugs fixed and improvements, compilation with -Weffc++
* Codon models
* Improved non-homogeneous classes
* Improved tree drawing classes
2009-06-10 - Julien Dutheil <jdutheil@birc.au.dk>
libbpp-phyl (1.8.0) unstable; urgency=low
* Several buf fixed and improvements.
* New support for Nexus tree files.
* New syntax for model description using keyvals.
2008-12-11 - Julien Dutheil <jdutheil@birc.au.dk>
libbpp-phyl (1.7.0) unstable; urgency=low
* Several bug fixed and improvements...
2008-09-24 - Julien Dutheil <jdutheil@birc.au.dk>
libbpp-phyl (1.6.0) unstable; urgency=low
* New +F protein models + bugs fixed.
2008-07-21 - Julien Dutheil <jdutheil@birc.au.dk>
libbpp-phyl (1.5.1) unstable; urgency=low
* Initial Release.

See Also

Package Description
libbpp-phyl-omics-dev_2.1.0-1_amd64.deb Bio++ Phylogenetics library: genomics components
libbpp-phyl-omics1_2.1.0-1_amd64.deb Bio++ Phylogenetics library: genomics components
libbpp-phyl9_2.1.0-1_amd64.deb Bio++ Phylogenetic library
libbpp-popgen-dev_2.1.0-1_amd64.deb Bio++ Population Genetics library development files
libbpp-popgen6_2.1.0-1_amd64.deb Bio++ Population Genetics library
libbpp-qt-dev_2.1.0-1_amd64.deb Bio++ Qt Graphic classes library development files
libbpp-qt1_2.1.0-1_amd64.deb Bio++ Qt Graphic classes library
libbpp-raa-dev_2.1.0-1_amd64.deb Bio++ Remote Acnuc Access library development files
libbpp-raa1_2.1.0-1_amd64.deb Bio++ Remote Acnuc Access library
libbpp-seq-dev_2.1.0-1_amd64.deb Bio++ Sequence library development files
libbpp-seq-omics-dev_2.1.0-1_amd64.deb Bio++ Sequence library: genomics components
libbpp-seq-omics1_2.1.0-1_amd64.deb Bio++ Sequence library: genomics components
libbpp-seq9_2.1.0-1_amd64.deb Bio++ Sequence library
libbrahe-1.3-3_1.3.2-4_amd64.deb heterogeneous C library of numeric functions
libbrahe-dev_1.3.2-4_amd64.deb heterogeneous C library of numeric functions
Advertisement
Advertisement