Date: Fri, 11 May 2018 00:05:16 +0000 (UTC) From: Joseph Mingrone <jrm@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r469604 - in head/biology: . hyphy hyphy/files Message-ID: <201805110005.w4B05GeK021252@repo.freebsd.org>
next in thread | raw e-mail | index | archive | help
Author: jrm Date: Fri May 11 00:05:16 2018 New Revision: 469604 URL: https://svnweb.freebsd.org/changeset/ports/469604 Log: New port, biology/hyphy: Hypothesis testing using Phylogenies WWW: http://www.hyphy.org/ Added: head/biology/hyphy/ head/biology/hyphy/Makefile (contents, props changed) head/biology/hyphy/distinfo (contents, props changed) head/biology/hyphy/files/ head/biology/hyphy/files/patch-src_core_calcnode.cpp (contents, props changed) head/biology/hyphy/files/patch-src_core_regex.cpp (contents, props changed) head/biology/hyphy/pkg-descr (contents, props changed) head/biology/hyphy/pkg-plist (contents, props changed) Modified: head/biology/Makefile (contents, props changed) Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Thu May 10 23:15:02 2018 (r469603) +++ head/biology/Makefile Fri May 11 00:05:16 2018 (r469604) @@ -42,6 +42,7 @@ SUBDIR += grappa SUBDIR += hmmer SUBDIR += htslib + SUBDIR += hyphy SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview Added: head/biology/hyphy/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hyphy/Makefile Fri May 11 00:05:16 2018 (r469604) @@ -0,0 +1,21 @@ +# $FreeBSD$ + +PORTNAME= hyphy +DISTVERSION= 2.3.12 +CATEGORIES= biology + +MAINTAINER= jrm@FreeBSD.org +COMMENT= Hypothesis testing using Phylogenies + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE + +ONLY_FOR_ARCHS= amd64 i386 + +LIB_DEPENDS= libcurl.so:ftp/curl + +USES= compiler:c++14-lang cmake:outsource localbase:ldflags ssl +USE_GITHUB= yes +GH_ACCOUNT= veg + +.include <bsd.port.mk> Added: head/biology/hyphy/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hyphy/distinfo Fri May 11 00:05:16 2018 (r469604) @@ -0,0 +1,3 @@ +TIMESTAMP = 1525983314 +SHA256 (veg-hyphy-2.3.12_GH0.tar.gz) = f78d5e7bcab2ad8405b9da9bdb4c7893ad7cd3290e1eec749855b064c6fc60fd +SIZE (veg-hyphy-2.3.12_GH0.tar.gz) = 7901009 Added: head/biology/hyphy/files/patch-src_core_calcnode.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hyphy/files/patch-src_core_calcnode.cpp Fri May 11 00:05:16 2018 (r469604) @@ -0,0 +1,11 @@ +--- src/core/calcnode.cpp.orig 2018-05-10 18:06:35 UTC ++++ src/core/calcnode.cpp +@@ -5932,7 +5932,7 @@ void _TheTree::TreePSRecurse (node<no + res << "0 0 0 setrgbcolor\n"; + } + +- if (iterator->is_root() == nil && layout == 1) { ++ if (!iterator->is_root() && layout == 1) { + res << (_String (-iterator->in_object.h) & ' ' & _String (-iterator->in_object.v) & " translate\n"); + } + } Added: head/biology/hyphy/files/patch-src_core_regex.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hyphy/files/patch-src_core_regex.cpp Fri May 11 00:05:16 2018 (r469604) @@ -0,0 +1,13 @@ +--- src/core/regex.cpp.orig 2018-05-10 18:11:45 UTC ++++ src/core/regex.cpp +@@ -31,10 +31,6 @@ + #pragma alloca + #endif + +-#if !defined REGEX_MALLOC && !defined __MINGW32__ +-#include <alloca.h> +-#endif +- + #ifndef _GNU_SOURCE + #define _GNU_SOURCE + #endif Added: head/biology/hyphy/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hyphy/pkg-descr Fri May 11 00:05:16 2018 (r469604) @@ -0,0 +1,9 @@ +HyPhy is an open-source software package for the analysis of genetic sequences +using techniques in phylogenetics, molecular evolution, and machine learning. It +features a rich scripting language for limitless customization of +analyses. Additionally, HyPhy features support for parallel computing +environments via message passing interface, MPI and it can be compiled as a +shared library and called from other programming environments such as Python and +R. + +WWW: http://www.hyphy.org/ Added: head/biology/hyphy/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hyphy/pkg-plist Fri May 11 00:05:16 2018 (r469604) @@ -0,0 +1,587 @@ +bin/HYPHYMP +lib/hyphy/ChartAddIns/Approximate_CDF +lib/hyphy/ChartAddIns/Column Operations +lib/hyphy/ChartAddIns/Complex Select Cells By Value +lib/hyphy/ChartAddIns/Contigency Table +lib/hyphy/ChartAddIns/Covariance +lib/hyphy/ChartAddIns/DBAddIns/DescriptiveStats.bf +lib/hyphy/ChartAddIns/DBAddIns/FromSQLFlatFile.bf +lib/hyphy/ChartAddIns/DBAddIns/HY_DBW_TemplateList +lib/hyphy/ChartAddIns/DBAddIns/ToChartWindow.bf +lib/hyphy/ChartAddIns/DBAddIns/ToConsole.bf +lib/hyphy/ChartAddIns/DBAddIns/ToFastaFile.bf +lib/hyphy/ChartAddIns/DBAddIns/ToFastaFileFromPandit.bf +lib/hyphy/ChartAddIns/DBAddIns/ToFrontierFastaFile.bf +lib/hyphy/ChartAddIns/DBAddIns/ToSQLFlatFile.bf +lib/hyphy/ChartAddIns/DBAddIns/ToTabFile.bf +lib/hyphy/ChartAddIns/Descriptive Statistics +lib/hyphy/ChartAddIns/Distribution Moments +lib/hyphy/ChartAddIns/DistributionAddIns/Event Posteriors +lib/hyphy/ChartAddIns/DistributionAddIns/Includes/posteriors.ibf +lib/hyphy/ChartAddIns/DistributionAddIns/Most Likely Class Assignment +lib/hyphy/ChartAddIns/DistributionAddIns/Posterior Distribution +lib/hyphy/ChartAddIns/DistributionAddIns/Posterior Moments +lib/hyphy/ChartAddIns/DistributionAddIns/Prior Moments +lib/hyphy/ChartAddIns/Gaussian Penalty Clustering +lib/hyphy/ChartAddIns/Goodness of Fit +lib/hyphy/ChartAddIns/Histogram +lib/hyphy/ChartAddIns/K-Mean Clustering +lib/hyphy/ChartAddIns/KH Resampler +lib/hyphy/ChartAddIns/Linear Fit +lib/hyphy/ChartAddIns/Mean Profile Plot +lib/hyphy/ChartAddIns/Median Profile Plot +lib/hyphy/ChartAddIns/Poisson Mixture Fit +lib/hyphy/ChartAddIns/Populate Cells +lib/hyphy/ChartAddIns/Profile Mean Clustering +lib/hyphy/ChartAddIns/Running Sum +lib/hyphy/ChartAddIns/Samplers/lhc.bf +lib/hyphy/ChartAddIns/Samplers/sir.bf +lib/hyphy/ChartAddIns/Samplers/srs.ibf +lib/hyphy/ChartAddIns/Select Cells By Index +lib/hyphy/ChartAddIns/Select Cells By Value +lib/hyphy/ChartAddIns/SingleColumn +lib/hyphy/ChartAddIns/Sort +lib/hyphy/DatapanelAddIns/Character Plot +lib/hyphy/DatapanelAddIns/Character Plot Two +lib/hyphy/DatapanelAddIns/Compare Subsets +lib/hyphy/DatapanelAddIns/Sequence Plot +lib/hyphy/DatapanelAddIns/TBD/Character Plot By Sequence +lib/hyphy/DatapanelAddIns/ibfs/char_colors.def +lib/hyphy/GeneticCodes/Alt_Yeast_Nuclear.cod +lib/hyphy/GeneticCodes/Ascidian_mtDNA.cod +lib/hyphy/GeneticCodes/Blepharisma_Nuclear.cod +lib/hyphy/GeneticCodes/Ciliate.cod +lib/hyphy/GeneticCodes/Echinoderm_mtDNA.cod +lib/hyphy/GeneticCodes/Euplotid_Nuclear.cod +lib/hyphy/GeneticCodes/Flatworm_mtDNA.cod +lib/hyphy/GeneticCodes/Invertebrate_mtDNA.cod +lib/hyphy/GeneticCodes/Mold_mtDNA.cod +lib/hyphy/GeneticCodes/Thraustochytrium_mtDNA.cod +lib/hyphy/GeneticCodes/Vertebratemtdna.cod +lib/hyphy/GeneticCodes/Yeast_mtDNA.cod +lib/hyphy/SubstitutionClasses/AAEFV/Equal +lib/hyphy/SubstitutionClasses/AAEFV/Estimated +lib/hyphy/SubstitutionClasses/AAEFV/Observed In Data Set +lib/hyphy/SubstitutionClasses/AAEFV/Observed In Partition +lib/hyphy/SubstitutionClasses/CodonEFV/Equal +lib/hyphy/SubstitutionClasses/CodonEFV/Observed Codon +lib/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 3 params. +lib/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 9 params. +lib/hyphy/SubstitutionClasses/Heterogeneity/2 Bin Discrete +lib/hyphy/SubstitutionClasses/Heterogeneity/Beta +lib/hyphy/SubstitutionClasses/Heterogeneity/Beta-Gamma +lib/hyphy/SubstitutionClasses/Heterogeneity/General Discrete +lib/hyphy/SubstitutionClasses/Heterogeneity/Half Normal +lib/hyphy/SubstitutionClasses/Heterogeneity/Lognormal +lib/hyphy/SubstitutionClasses/NucEFV/Equal +lib/hyphy/SubstitutionClasses/NucEFV/Estimated +lib/hyphy/SubstitutionClasses/NucEFV/Observed In Data Set +lib/hyphy/SubstitutionClasses/NucEFV/Observed In Partition +lib/hyphy/SubstitutionClasses/aa.bf +lib/hyphy/SubstitutionClasses/codon.bf +lib/hyphy/SubstitutionClasses/dinuc.bf +lib/hyphy/SubstitutionClasses/nuc.bf +lib/hyphy/SubstitutionModels/Aminoacid/Dayhoff.mdl +lib/hyphy/SubstitutionModels/Aminoacid/EIAA.mdl +lib/hyphy/SubstitutionModels/Aminoacid/Fitness.mdl +lib/hyphy/SubstitutionModels/Aminoacid/Jones.mdl +lib/hyphy/SubstitutionModels/Aminoacid/mtREV.mdl +lib/hyphy/SubstitutionModels/Binary/F81.mdl +lib/hyphy/SubstitutionModels/Codon/GY94_3x4.mdl +lib/hyphy/SubstitutionModels/Codon/Lineage_MG94xHKY85.mdl +lib/hyphy/SubstitutionModels/Codon/MG94.mdl +lib/hyphy/SubstitutionModels/Codon/MG94REVOmegaCF3x4.mdl +lib/hyphy/SubstitutionModels/Codon/MG94_3x4.mdl +lib/hyphy/SubstitutionModels/Codon/MG94_HKY85x3_4.mdl +lib/hyphy/SubstitutionModels/Codon/MG94_REV_3x4.mdl +lib/hyphy/SubstitutionModels/Codon/MG94xHKY85_3x4_2Rates.mdl +lib/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV.mdl +lib/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV_GDD.mdl +lib/hyphy/SubstitutionModels/Codon/MG94xTN93_3x4.mdl +lib/hyphy/SubstitutionModels/Nucleotide/EFVEstimated.ibf +lib/hyphy/SubstitutionModels/Nucleotide/F81.mdl +lib/hyphy/SubstitutionModels/Nucleotide/HKY85.mdl +lib/hyphy/SubstitutionModels/Nucleotide/REV.mdl +lib/hyphy/SubstitutionModels/Nucleotide/REVBetaGamma.mdl +lib/hyphy/SubstitutionModels/Nucleotide/TrN.mdl +lib/hyphy/SubstitutionModels/User/Nucleotide/JC69 +lib/hyphy/SubstitutionModels/User/Nucleotide/K2P +lib/hyphy/TemplateBatchFiles/2RatesAnalyses/GY94.mdl +lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94GY94xREV_PARRIS_syn3.mdl +lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREV.mdl +lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate.mdl +lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate_Multirate.mdl +lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M1.def +lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M2.def +lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M3.def +lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_syn3.def +lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_synvar.def +lib/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGenerator.bf +lib/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGeneratorNoPS.bf +lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma1.def +lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2+Inv.def +lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2.def +lib/hyphy/TemplateBatchFiles/454.bf +lib/hyphy/TemplateBatchFiles/AAModelComparison.bf +lib/hyphy/TemplateBatchFiles/AddABias.ibf +lib/hyphy/TemplateBatchFiles/AnalyzeCodonData.bf +lib/hyphy/TemplateBatchFiles/AnalyzeCodonDataMPI.bf +lib/hyphy/TemplateBatchFiles/AnalyzeDiNucData.bf +lib/hyphy/TemplateBatchFiles/AnalyzeNucDataFreq.bf +lib/hyphy/TemplateBatchFiles/AnalyzeNucDataFreq2.bf +lib/hyphy/TemplateBatchFiles/AnalyzeNucProtData.bf +lib/hyphy/TemplateBatchFiles/AnalyzeNucProtData2.bf +lib/hyphy/TemplateBatchFiles/BGM.bf +lib/hyphy/TemplateBatchFiles/BS2007.bf +lib/hyphy/TemplateBatchFiles/BUSTED-SRV.bf +lib/hyphy/TemplateBatchFiles/BivariateCodonRateAnalysis.bf +lib/hyphy/TemplateBatchFiles/BranchClassDNDS.bf +lib/hyphy/TemplateBatchFiles/BranchSiteREL.bf +lib/hyphy/TemplateBatchFiles/BranchSiteRELMultiModel.bf +lib/hyphy/TemplateBatchFiles/BranchSwap.bf +lib/hyphy/TemplateBatchFiles/CleanGaps.bf +lib/hyphy/TemplateBatchFiles/CleanStopCodons.bf +lib/hyphy/TemplateBatchFiles/ClusterAnalysis.bf +lib/hyphy/TemplateBatchFiles/ClusterByDistanceRange.bf +lib/hyphy/TemplateBatchFiles/CodonBivariateRateProcessor.bf +lib/hyphy/TemplateBatchFiles/CodonModelCompare.bf +lib/hyphy/TemplateBatchFiles/CodonToProtein.bf +lib/hyphy/TemplateBatchFiles/CodonUsageBias.bf +lib/hyphy/TemplateBatchFiles/CompareSelectivePressure.bf +lib/hyphy/TemplateBatchFiles/CompareSelectivePressureIVL.bf +lib/hyphy/TemplateBatchFiles/ConvertDataFile.bf +lib/hyphy/TemplateBatchFiles/DatedTipsMolecularClock.bf +lib/hyphy/TemplateBatchFiles/DirectionalREL.bf +lib/hyphy/TemplateBatchFiles/DirectionalREL_MF.bf +lib/hyphy/TemplateBatchFiles/DistanceMatrix.bf +lib/hyphy/TemplateBatchFiles/DistanceMatrix_Splits.bf +lib/hyphy/TemplateBatchFiles/Distances/CodonTools.def +lib/hyphy/TemplateBatchFiles/Distances/CodonTools2.def +lib/hyphy/TemplateBatchFiles/Distances/CodonToolsMain.def +lib/hyphy/TemplateBatchFiles/Distances/JC69 +lib/hyphy/TemplateBatchFiles/Distances/K2P +lib/hyphy/TemplateBatchFiles/Distances/K2P_RV +lib/hyphy/TemplateBatchFiles/Distances/Modified_Nei_Gojobori +lib/hyphy/TemplateBatchFiles/Distances/Nei_Gojobori +lib/hyphy/TemplateBatchFiles/Distances/PC +lib/hyphy/TemplateBatchFiles/Distances/PC_MH +lib/hyphy/TemplateBatchFiles/Distances/PC_RV +lib/hyphy/TemplateBatchFiles/Distances/T3P +lib/hyphy/TemplateBatchFiles/Distances/TN84 +lib/hyphy/TemplateBatchFiles/Distances/TN93 +lib/hyphy/TemplateBatchFiles/Distances/TN93_RV +lib/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ +lib/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ_FR +lib/hyphy/TemplateBatchFiles/Distances/p_Distance +lib/hyphy/TemplateBatchFiles/Distances/p_Distance_aa +lib/hyphy/TemplateBatchFiles/Distances/p_Distance_binary +lib/hyphy/TemplateBatchFiles/Distances/p_Distance_codon +lib/hyphy/TemplateBatchFiles/F_ST.bf +lib/hyphy/TemplateBatchFiles/FitnessAAModels.bf +lib/hyphy/TemplateBatchFiles/GADatedClock.bf +lib/hyphy/TemplateBatchFiles/GADatedClock.ibf +lib/hyphy/TemplateBatchFiles/GADatedClockProcessor.bf +lib/hyphy/TemplateBatchFiles/GADatedClockProcessorM.bf +lib/hyphy/TemplateBatchFiles/GARD.bf +lib/hyphy/TemplateBatchFiles/GARDProcessor.bf +lib/hyphy/TemplateBatchFiles/GARD_GA_CHC.ibf +lib/hyphy/TemplateBatchFiles/GARecomb.bf +lib/hyphy/TemplateBatchFiles/GA_CHC.ibf +lib/hyphy/TemplateBatchFiles/GA_CHC_Binary.ibf +lib/hyphy/TemplateBatchFiles/GA_CHC_kernel.ibf +lib/hyphy/TemplateBatchFiles/GUI/crayolaColors.def +lib/hyphy/TemplateBatchFiles/Gateaux.bf +lib/hyphy/TemplateBatchFiles/Gateaux2.bf +lib/hyphy/TemplateBatchFiles/GateauxMR.bf +lib/hyphy/TemplateBatchFiles/KHTest.bf +lib/hyphy/TemplateBatchFiles/Kernel_PCA.bf +lib/hyphy/TemplateBatchFiles/Kernel_k_means.bf +lib/hyphy/TemplateBatchFiles/Kernel_support.ibf +lib/hyphy/TemplateBatchFiles/LEISR.bf +lib/hyphy/TemplateBatchFiles/LHT.bf +lib/hyphy/TemplateBatchFiles/LRTRecombTest.bf +lib/hyphy/TemplateBatchFiles/LZ_Complexity.bf +lib/hyphy/TemplateBatchFiles/LocalBranchSiteTest.bf +lib/hyphy/TemplateBatchFiles/LocalMolClock.bf +lib/hyphy/TemplateBatchFiles/MEDS.bf +lib/hyphy/TemplateBatchFiles/MEME_mf.bf +lib/hyphy/TemplateBatchFiles/MFPSreader.def +lib/hyphy/TemplateBatchFiles/MFPositiveSelection.bf +lib/hyphy/TemplateBatchFiles/MFPositiveSelectionPooled.bf +lib/hyphy/TemplateBatchFiles/MGvsGY.bf +lib/hyphy/TemplateBatchFiles/MaxChi2.bf +lib/hyphy/TemplateBatchFiles/MergeSequences.bf +lib/hyphy/TemplateBatchFiles/MergeSites.bf +lib/hyphy/TemplateBatchFiles/ModelSelectorAAProcessor.bf +lib/hyphy/TemplateBatchFiles/ModelSelectorBranch.bf +lib/hyphy/TemplateBatchFiles/ModelSelectorCodon.bf +lib/hyphy/TemplateBatchFiles/ModelSelectorCodon.ibf +lib/hyphy/TemplateBatchFiles/ModelSelectorCodonProcessor.bf +lib/hyphy/TemplateBatchFiles/ModelSelectorRNA.bf +lib/hyphy/TemplateBatchFiles/ModelSelectorRNA_1.bf +lib/hyphy/TemplateBatchFiles/ModelTest.bf +lib/hyphy/TemplateBatchFiles/MolClockAllRoots.bf +lib/hyphy/TemplateBatchFiles/MolecularClock.bf +lib/hyphy/TemplateBatchFiles/NeighborJoining.bf +lib/hyphy/TemplateBatchFiles/NielsenYang.bf +lib/hyphy/TemplateBatchFiles/NucModelCompare.bf +lib/hyphy/TemplateBatchFiles/PARRIS.bf +lib/hyphy/TemplateBatchFiles/PairwiseRelativeRate.bf +lib/hyphy/TemplateBatchFiles/PairwiseRelativeRatio.bf +lib/hyphy/TemplateBatchFiles/PairwiseSiteDiversity.bf +lib/hyphy/TemplateBatchFiles/PartitionDataFile.bf +lib/hyphy/TemplateBatchFiles/PartitionRateComparison.bf +lib/hyphy/TemplateBatchFiles/Phylohandbook.bf +lib/hyphy/TemplateBatchFiles/Plato.bf +lib/hyphy/TemplateBatchFiles/PositiveSelectionLI.bf +lib/hyphy/TemplateBatchFiles/ProteinAnalyses/README_relative_prot_rates.md +lib/hyphy/TemplateBatchFiles/ProteinAnalyses/relative_prot_rates.bf +lib/hyphy/TemplateBatchFiles/QuickSelectionDetection-MEME-internal.bf +lib/hyphy/TemplateBatchFiles/QuickSelectionDetection.bf +lib/hyphy/TemplateBatchFiles/QuickSelectionDetectionMF.bf +lib/hyphy/TemplateBatchFiles/RateClassCounter.bf +lib/hyphy/TemplateBatchFiles/ReduceDataSetMatrix.bf +lib/hyphy/TemplateBatchFiles/RelativeRate.bf +lib/hyphy/TemplateBatchFiles/RelativeRateL.bf +lib/hyphy/TemplateBatchFiles/RelativeRatio.bf +lib/hyphy/TemplateBatchFiles/SGASimProcessor.bf +lib/hyphy/TemplateBatchFiles/SGEmulator.bf +lib/hyphy/TemplateBatchFiles/SGEmulator_MF.bf +lib/hyphy/TemplateBatchFiles/SGIvL.bf +lib/hyphy/TemplateBatchFiles/SSRatesTest.bf +lib/hyphy/TemplateBatchFiles/SampleProcessor.bf +lib/hyphy/TemplateBatchFiles/Samplers/lhc.bf +lib/hyphy/TemplateBatchFiles/Samplers/lhc_supp.ibf +lib/hyphy/TemplateBatchFiles/Samplers/sir.bf +lib/hyphy/TemplateBatchFiles/Samplers/srs.ibf +lib/hyphy/TemplateBatchFiles/SandNSAmbigs.bf +lib/hyphy/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf +lib/hyphy/TemplateBatchFiles/SelectionAnalyses/BranchSiteREL.bf +lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FEL-contrast.bf +lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FEL.bf +lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf +lib/hyphy/TemplateBatchFiles/SelectionAnalyses/MEME.bf +lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX-Groups.bf +lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX-SRV.bf +lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX.bf +lib/hyphy/TemplateBatchFiles/SelectionAnalyses/SLAC.bf +lib/hyphy/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf +lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf +lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf +lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf +lib/hyphy/TemplateBatchFiles/SelectionLRT.bf +lib/hyphy/TemplateBatchFiles/SeqAlignShared.ibf +lib/hyphy/TemplateBatchFiles/SeqAlignment.bf +lib/hyphy/TemplateBatchFiles/SeqAlignmentCodon.bf +lib/hyphy/TemplateBatchFiles/SeqAlignmentCodonShared.ibf +lib/hyphy/TemplateBatchFiles/SeqAlignmentNuc.bf +lib/hyphy/TemplateBatchFiles/SeqAlignmentNucShared.ibf +lib/hyphy/TemplateBatchFiles/SeqAlignmentProt.bf +lib/hyphy/TemplateBatchFiles/SeqAlignmentTop75.bf +lib/hyphy/TemplateBatchFiles/SequentialAddition.bf +lib/hyphy/TemplateBatchFiles/SequentialAddition.ibf +lib/hyphy/TemplateBatchFiles/SimilarityPlot.bf +lib/hyphy/TemplateBatchFiles/SimmondsAI.bf +lib/hyphy/TemplateBatchFiles/SimpleMutationCounter.bf +lib/hyphy/TemplateBatchFiles/SingleBreakpointRecomb-2.bf +lib/hyphy/TemplateBatchFiles/SingleBreakpointRecomb.bf +lib/hyphy/TemplateBatchFiles/SiteRates.bf +lib/hyphy/TemplateBatchFiles/SiteRates2.bf +lib/hyphy/TemplateBatchFiles/SlatkinMaddison-2parts.bf +lib/hyphy/TemplateBatchFiles/SlatkinMaddison.bf +lib/hyphy/TemplateBatchFiles/SlidingNucWindow.bf +lib/hyphy/TemplateBatchFiles/SlidingWindowAnalysis.bf +lib/hyphy/TemplateBatchFiles/SplitSequencesByPattern.bf +lib/hyphy/TemplateBatchFiles/StarDecomposition.bf +lib/hyphy/TemplateBatchFiles/StrandGRMTest.bf +lib/hyphy/TemplateBatchFiles/StripStopCodons.bf +lib/hyphy/TemplateBatchFiles/SubtreeSelectionComparison.bf +lib/hyphy/TemplateBatchFiles/TemplateModels/190 +lib/hyphy/TemplateBatchFiles/TemplateModels/BranchSiteTemplate.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/CF3x4.bf +lib/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA_empirical.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff_F.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/Default +lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F+omega.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F3x4.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+MLFREQS.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/ECM.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/EIAA.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/EIAAFreq.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/EX.dat +lib/hyphy/TemplateBatchFiles/TemplateModels/EX.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/BLOSUM62 +lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/Dayhoff +lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/H5N1 +lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVBetween +lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVWithin +lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/IAV +lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/JTT +lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LCAP +lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LG +lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/MtArt +lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/VT +lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/WAG +lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/cpREV +lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/modellist.ibf +lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtMAM +lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtREV24 +lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/rtREV +lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECM +lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECMu +lib/hyphy/TemplateBatchFiles/TemplateModels/F81.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/F81_binary.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/F84.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/F84P.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/GRM.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/GY94.ibf +lib/hyphy/TemplateBatchFiles/TemplateModels/GY94.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/GY94customF3x4.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/GY94w9.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween+F.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.ibf +lib/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin+F.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.ibf +lib/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/HKY85.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/JC69.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/JC69_binary.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/Jones.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/Jones_F.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/K2P.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/K3ST.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/LCAP.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/MEC.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/MG94.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/MG94custom.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/MG94customCF3x4.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/MG94customF1x4.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/MG94customFreqs.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAA.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAF61.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAF61multiple.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAFreqs.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAUserFreqs.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wEX.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/MG94with9freqs.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/MG94x2.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/MGFreqsEstimator.ibf +lib/hyphy/TemplateBatchFiles/TemplateModels/MGwAA.ibf +lib/hyphy/TemplateBatchFiles/TemplateModels/MGwEX.ibf +lib/hyphy/TemplateBatchFiles/TemplateModels/NRM+Freqs.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/NRM.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/PCH +lib/hyphy/TemplateBatchFiles/TemplateModels/RNA16.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/RNA16A +lib/hyphy/TemplateBatchFiles/TemplateModels/RNA16SvH.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/RNAEqualInput +lib/hyphy/TemplateBatchFiles/TemplateModels/RNAF81 +lib/hyphy/TemplateBatchFiles/TemplateModels/RNAMuse95.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/RNAREV +lib/hyphy/TemplateBatchFiles/TemplateModels/RNAREV_1 +lib/hyphy/TemplateBatchFiles/TemplateModels/S4 +lib/hyphy/TemplateBatchFiles/TemplateModels/STGRM.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/TrN.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/UniversalCode.def +lib/hyphy/TemplateBatchFiles/TemplateModels/WAG.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/WAG_F.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/Yang2000Distributions.def +lib/hyphy/TemplateBatchFiles/TemplateModels/chooseGeneticCode.def +lib/hyphy/TemplateBatchFiles/TemplateModels/custm4x4.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/defineGamma.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/defineHM.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/fitness.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters2.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters3.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters4.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters5.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/models.lst +lib/hyphy/TemplateBatchFiles/TemplateModels/mtMAM.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/mtMAM_F.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/mtREV.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/mtREV_24.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/mtREV_24_F.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/reducedREV.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/rtREV.mdl +lib/hyphy/TemplateBatchFiles/TemplateModels/rtREV_F.mdl +lib/hyphy/TemplateBatchFiles/TestBranchDNDS.bf +lib/hyphy/TemplateBatchFiles/TestClade.bf +lib/hyphy/TemplateBatchFiles/TestCladeMeans.bf +lib/hyphy/TemplateBatchFiles/TopologySearch.bf +lib/hyphy/TemplateBatchFiles/TopologySearchConstrained.bf +lib/hyphy/TemplateBatchFiles/TreeCorrelationCoefficients.bf +lib/hyphy/TemplateBatchFiles/TreeTools.ibf +lib/hyphy/TemplateBatchFiles/UpperBound.bf +lib/hyphy/TemplateBatchFiles/Utility/AncestralMapper.bf +lib/hyphy/TemplateBatchFiles/Utility/BranchLengthFitters.bf +lib/hyphy/TemplateBatchFiles/Utility/CoalescentPostProcessor.bf +lib/hyphy/TemplateBatchFiles/Utility/CodonTools.bf +lib/hyphy/TemplateBatchFiles/Utility/DBTools.ibf +lib/hyphy/TemplateBatchFiles/Utility/DescriptiveStatistics.bf +lib/hyphy/TemplateBatchFiles/Utility/GrabBag.bf +lib/hyphy/TemplateBatchFiles/Utility/HXB2Mapper.bf +lib/hyphy/TemplateBatchFiles/Utility/LocalMGREV.bf +lib/hyphy/TemplateBatchFiles/Utility/LocalMGREVMLFreqs.bf +lib/hyphy/TemplateBatchFiles/Utility/MPITools.bf +lib/hyphy/TemplateBatchFiles/Utility/NJ.bf +lib/hyphy/TemplateBatchFiles/Utility/PS_Plotters.bf +lib/hyphy/TemplateBatchFiles/Utility/PostScript.bf +lib/hyphy/TemplateBatchFiles/Utility/ProbabilityDistributions.bf +lib/hyphy/TemplateBatchFiles/Utility/ReadDelimitedFiles.bf +lib/hyphy/TemplateBatchFiles/Utility/TreeFunctions.bf +lib/hyphy/TemplateBatchFiles/Utility/WriteDelimitedFiles.bf +lib/hyphy/TemplateBatchFiles/WANC.bf +lib/hyphy/TemplateBatchFiles/WebUpdate.bf +lib/hyphy/TemplateBatchFiles/YangNielsenBranchSite2005.bf +lib/hyphy/TemplateBatchFiles/_BMS_Aux.ibf +lib/hyphy/TemplateBatchFiles/_CMS_Aux.ibf +lib/hyphy/TemplateBatchFiles/_MFReader_.ibf +lib/hyphy/TemplateBatchFiles/_MSCOneStep.ibf +lib/hyphy/TemplateBatchFiles/_tipDater.ibf +lib/hyphy/TemplateBatchFiles/bayesgraph.ibf +lib/hyphy/TemplateBatchFiles/binomial.ibf +lib/hyphy/TemplateBatchFiles/branchSwappingFunctions.bf +lib/hyphy/TemplateBatchFiles/categoryEcho.bf +lib/hyphy/TemplateBatchFiles/chooseDistanceFormula.def +lib/hyphy/TemplateBatchFiles/dNdSBivariateRateAnalysis.bf +lib/hyphy/TemplateBatchFiles/dNdSBivariateRateAnalysis_CompareDS.bf +lib/hyphy/TemplateBatchFiles/dNdSDistributionComparison.bf +lib/hyphy/TemplateBatchFiles/dNdSDistributionComparisonPartitions.bf +lib/hyphy/TemplateBatchFiles/dNdSRateAnalysis.bf +lib/hyphy/TemplateBatchFiles/dNdSRateAnalysis_MF.bf +lib/hyphy/TemplateBatchFiles/dNdSResultProcessor.bf +lib/hyphy/TemplateBatchFiles/dSdNTreeTools.ibf +lib/hyphy/TemplateBatchFiles/distanceMethodNPBootstrap.bf +lib/hyphy/TemplateBatchFiles/distanceRMethodNPBootstrap.bf +lib/hyphy/TemplateBatchFiles/doNNISwap.bf +lib/hyphy/TemplateBatchFiles/doSPRSwap.bf +lib/hyphy/TemplateBatchFiles/files.lst +lib/hyphy/TemplateBatchFiles/globalChecker.ibf +lib/hyphy/TemplateBatchFiles/heuristicMethodNPBootstrap.bf +lib/hyphy/TemplateBatchFiles/last.date +lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf +lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf +lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf +lib/hyphy/TemplateBatchFiles/libv3/convenience/math.bf +lib/hyphy/TemplateBatchFiles/libv3/convenience/matrix.bf +lib/hyphy/TemplateBatchFiles/libv3/convenience/random.bf +lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf +lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf +lib/hyphy/TemplateBatchFiles/libv3/models/DNA/GTR.bf +lib/hyphy/TemplateBatchFiles/libv3/models/DNA/HKY85.bf +lib/hyphy/TemplateBatchFiles/libv3/models/DNA/JC69.bf +lib/hyphy/TemplateBatchFiles/libv3/models/binary.bf +lib/hyphy/TemplateBatchFiles/libv3/models/binary/charbinary.bf +lib/hyphy/TemplateBatchFiles/libv3/models/codon.bf +lib/hyphy/TemplateBatchFiles/libv3/models/codon/BS_REL.bf +lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV.bf +lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf +lib/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf +lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf +lib/hyphy/TemplateBatchFiles/libv3/models/protein.bf +lib/hyphy/TemplateBatchFiles/libv3/models/protein/REV.bf +lib/hyphy/TemplateBatchFiles/libv3/models/protein/empirical.bf +lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/HIV.ibf +lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/JC69.ibf +lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/JTT.ibf +lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/LG.ibf +lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/WAG.ibf +lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/gcpREV.ibf +lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/mt.ibf +lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrix2dict_aux.bf +lib/hyphy/TemplateBatchFiles/libv3/models/rate_variation.bf +lib/hyphy/TemplateBatchFiles/libv3/stats.bf +lib/hyphy/TemplateBatchFiles/libv3/tasks/alignments.bf +lib/hyphy/TemplateBatchFiles/libv3/tasks/ancestral.bf +lib/hyphy/TemplateBatchFiles/libv3/tasks/estimators.bf +lib/hyphy/TemplateBatchFiles/libv3/tasks/genetic_code.bf +lib/hyphy/TemplateBatchFiles/libv3/tasks/mpi.bf +lib/hyphy/TemplateBatchFiles/libv3/tasks/trees.bf +lib/hyphy/TemplateBatchFiles/molclockBootstrap.bf +lib/hyphy/TemplateBatchFiles/pairwiseDistanceEstimator.ibf +lib/hyphy/TemplateBatchFiles/pairwiseDistanceEstimatorCounter.ibf +lib/hyphy/TemplateBatchFiles/partitionSequences.ibf +lib/hyphy/TemplateBatchFiles/post_ancestors.bf +lib/hyphy/TemplateBatchFiles/post_counting.bf +lib/hyphy/TemplateBatchFiles/post_covariance.bf +lib/hyphy/TemplateBatchFiles/post_dNdS.bf +lib/hyphy/TemplateBatchFiles/post_lfprofile.bf +lib/hyphy/TemplateBatchFiles/post_npbs.bf +lib/hyphy/TemplateBatchFiles/post_pbs.bf +lib/hyphy/TemplateBatchFiles/post_sampler.bf +lib/hyphy/TemplateBatchFiles/post_saveResults.bf +lib/hyphy/TemplateBatchFiles/post_sns.bf +lib/hyphy/TemplateBatchFiles/post_variance.bf +lib/hyphy/TemplateBatchFiles/post_viewResults.bf +lib/hyphy/TemplateBatchFiles/postprocessors.lst +lib/hyphy/TemplateBatchFiles/qndhelper1.ibf +lib/hyphy/TemplateBatchFiles/qndhelper1_mf.ibf +lib/hyphy/TemplateBatchFiles/qndhelper2.ibf +lib/hyphy/TemplateBatchFiles/qndhelper2_mf.ibf +lib/hyphy/TemplateBatchFiles/qndhelper3.ibf +lib/hyphy/TemplateBatchFiles/qndhelper4.ibf +lib/hyphy/TemplateBatchFiles/queryTree.bf +lib/hyphy/TemplateBatchFiles/readIndexFile.bf +lib/hyphy/TemplateBatchFiles/relrateBootstrap.bf +lib/hyphy/TemplateBatchFiles/relrateBootstrapL.bf +lib/hyphy/TemplateBatchFiles/relratioBootstrap.bf +lib/hyphy/TemplateBatchFiles/selectModelParameters.bf +lib/hyphy/TemplateBatchFiles/simpleBootstrap.bf +lib/hyphy/TopologyInference/Exhaustive_Search +lib/hyphy/TopologyInference/Neighbor_Joining +lib/hyphy/TopologyInference/Sequential_Addition +lib/hyphy/TopologyInference/Star_Decomposition +lib/hyphy/TopologyInference/Support/branchSwappingFunctions.bf +lib/hyphy/TopologyInference/Support/doNNISwap.bf +lib/hyphy/TopologyInference/Support/doSPRSwap.bf +lib/hyphy/TreeAddIns/Splits +lib/hyphy/TreeAddIns/Tree Statistics +lib/hyphy/UserAddins/AAContent +lib/hyphy/UserAddins/BatchFileByURL +lib/hyphy/UserAddins/BranchLengthCI +lib/hyphy/UserAddins/CodonMutationToTreeMapper +lib/hyphy/UserAddins/CountSubstitutions +lib/hyphy/UserAddins/ExportLikelihoodFunction +lib/hyphy/UserAddins/GenBankSequences +lib/hyphy/UserAddins/Includes/ChooseALF.ibf +lib/hyphy/UserAddins/Includes/MappersHelp.ibf +lib/hyphy/UserAddins/Includes/MappersHelpAA.ibf +lib/hyphy/UserAddins/LRT +lib/hyphy/UserAddins/ListUserFunctions +lib/hyphy/UserAddins/MapSubstitutions +lib/hyphy/UserAddins/MeanPairwiseDivergence +lib/hyphy/UserAddins/MeanPairwiseDivergenceSubset +lib/hyphy/UserAddins/ModelCounter +lib/hyphy/UserAddins/OldAddins/AAMutationCounter +lib/hyphy/UserAddins/OldAddins/CodonMutationToTreeMapper.bf +lib/hyphy/UserAddins/OldAddins/ColorPSTree +lib/hyphy/UserAddins/OldAddins/ConvergentAndParallel +lib/hyphy/UserAddins/OldAddins/CopyBranchLengths +lib/hyphy/UserAddins/OldAddins/DashPSTree +lib/hyphy/UserAddins/OldAddins/ExpsPerDirection +lib/hyphy/UserAddins/OldAddins/FilterAssignments +lib/hyphy/UserAddins/OldAddins/InferredAASubstitutionsCounter +lib/hyphy/UserAddins/OldAddins/LocaldNdS +lib/hyphy/UserAddins/OldAddins/ModelFitSummary +lib/hyphy/UserAddins/OldAddins/ModelFitSummaryAA +lib/hyphy/UserAddins/OldAddins/Multiclass DN DS inference +lib/hyphy/UserAddins/OldAddins/PartitionBranchesByClasses +lib/hyphy/UserAddins/OldAddins/PredictivePosteriorP +lib/hyphy/UserAddins/OldAddins/RNARateMatrix +lib/hyphy/UserAddins/OldAddins/SimulateAndTabDN_DS +lib/hyphy/UserAddins/OldAddins/SimulateFromLF +lib/hyphy/UserAddins/OldAddins/TreeLengthConstraint +lib/hyphy/UserAddins/OldAddins/dNanddSTrees.bf +lib/hyphy/UserAddins/OldAddins/dS and dN factors +lib/hyphy/UserAddins/RecombinationProcessor.bf +lib/hyphy/UserAddins/SimulateFromLF +lib/hyphy/UserAddins/Tidbits +lib/hyphy/data/brown.nuc +lib/hyphy/data/integrase_BDA.nex +lib/hyphy/data/p51.aa +lib/hyphy/data/p51.nex
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?201805110005.w4B05GeK021252>