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


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Description

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

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

    Download

    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

    • /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.

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