From owner-svn-ports-head@freebsd.org Fri Feb 21 12:22:18 2020 Return-Path: Delivered-To: svn-ports-head@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id D507525C250; Fri, 21 Feb 2020 12:22:18 +0000 (UTC) (envelope-from jrm@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits) client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 48P9ZL3ZTZz4XWl; Fri, 21 Feb 2020 12:22:18 +0000 (UTC) (envelope-from jrm@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 64564AB29; Fri, 21 Feb 2020 12:22:18 +0000 (UTC) (envelope-from jrm@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id 01LCMIC5049991; Fri, 21 Feb 2020 12:22:18 GMT (envelope-from jrm@FreeBSD.org) Received: (from jrm@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id 01LCMH68049988; Fri, 21 Feb 2020 12:22:17 GMT (envelope-from jrm@FreeBSD.org) Message-Id: <202002211222.01LCMH68049988@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: jrm set sender to jrm@FreeBSD.org using -f From: Joseph Mingrone Date: Fri, 21 Feb 2020 12:22:17 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r526622 - in head/biology/hyphy: . files X-SVN-Group: ports-head X-SVN-Commit-Author: jrm X-SVN-Commit-Paths: in head/biology/hyphy: . files X-SVN-Commit-Revision: 526622 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 21 Feb 2020 12:22:18 -0000 Author: jrm Date: Fri Feb 21 12:22:17 2020 New Revision: 526622 URL: https://svnweb.freebsd.org/changeset/ports/526622 Log: biology/hyphy: Update to version 2.5.4 Upstream changes: https://github.com/veg/hyphy/releases Added: head/biology/hyphy/files/patch-src_core_dataset.cpp (contents, props changed) Deleted: head/biology/hyphy/files/patch-src_core_regex.cpp Modified: head/biology/hyphy/Makefile (contents, props changed) head/biology/hyphy/distinfo (contents, props changed) head/biology/hyphy/pkg-plist (contents, props changed) Modified: head/biology/hyphy/Makefile ============================================================================== --- head/biology/hyphy/Makefile Fri Feb 21 12:01:28 2020 (r526621) +++ head/biology/hyphy/Makefile Fri Feb 21 12:22:17 2020 (r526622) @@ -1,9 +1,7 @@ # $FreeBSD$ PORTNAME= hyphy -DISTVERSION= 2.3.14-16 -PORTREVISION= 2 -DISTVERSIONSUFFIX= -g3d88d3e6 +DISTVERSION= 2.5.4 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org @@ -16,7 +14,7 @@ ONLY_FOR_ARCHS= amd64 i386 LIB_DEPENDS= libcurl.so:ftp/curl -USES= compiler:c++14-lang cmake localbase:ldflags ssl +USES= compiler:openmp cmake localbase:ldflags ssl USE_GITHUB= yes GH_ACCOUNT= veg Modified: head/biology/hyphy/distinfo ============================================================================== --- head/biology/hyphy/distinfo Fri Feb 21 12:01:28 2020 (r526621) +++ head/biology/hyphy/distinfo Fri Feb 21 12:22:17 2020 (r526622) @@ -1,3 +1,3 @@ -TIMESTAMP = 1540036335 -SHA256 (veg-hyphy-2.3.14-16-g3d88d3e6_GH0.tar.gz) = 459cd0a261ae5f31dc230847acbd294a4dc1e17fa69ef0c3db173c2b8808c826 -SIZE (veg-hyphy-2.3.14-16-g3d88d3e6_GH0.tar.gz) = 8041349 +TIMESTAMP = 1582224548 +SHA256 (veg-hyphy-2.5.4_GH0.tar.gz) = ddd0a1911ebfe88bff841095e8ddf641b7cd0e5bec043b7b185069067add17f3 +SIZE (veg-hyphy-2.5.4_GH0.tar.gz) = 6177551 Added: head/biology/hyphy/files/patch-src_core_dataset.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hyphy/files/patch-src_core_dataset.cpp Fri Feb 21 12:22:17 2020 (r526622) @@ -0,0 +1,11 @@ +--- src/core/dataset.cpp.orig 2020-02-20 18:58:13 UTC ++++ src/core/dataset.cpp +@@ -700,7 +700,7 @@ void _DataSet::MatchIndices(_Formula &f, _SimpleList & + receptacle << i; + } + } +- v->SetValue(new _Constant(0.0), nil); ++ v->SetValue(new _Constant(0.0), false); + } + + //_________________________________________________________ Modified: head/biology/hyphy/pkg-plist ============================================================================== --- head/biology/hyphy/pkg-plist Fri Feb 21 12:01:28 2020 (r526621) +++ head/biology/hyphy/pkg-plist Fri Feb 21 12:22:17 2020 (r526622) @@ -1,52 +1,5 @@ -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 +bin/hyphy +lib/hyphy/TemplateBatchFiles/simpleBootstrap.bf lib/hyphy/GeneticCodes/Alt_Yeast_Nuclear.cod lib/hyphy/GeneticCodes/Ascidian_mtDNA.cod lib/hyphy/GeneticCodes/Blepharisma_Nuclear.cod @@ -121,24 +74,16 @@ lib/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGe 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 @@ -146,15 +91,8 @@ 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 @@ -178,47 +116,34 @@ lib/hyphy/TemplateBatchFiles/Distances/p_Distance_bina 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/Miscellaneous/phylohandbook/BranchAPriori.bf +lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/CountSubstitutions.bf +lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/EffectOfTopology.bf +lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/ErrorEstimates.bf +lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/LRT.bf +lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/LocalvsGlobal.bf +lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/NeutralExpectation.bf +lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/NucleotideBiases.bf +lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/Phylohandbook.bf +lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/WhatsInTheMean.bf +lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/dSdN.bf +lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/Drosophilia_adh.nex +lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/H5N1_HA_5.nex lib/hyphy/TemplateBatchFiles/ModelTest.bf lib/hyphy/TemplateBatchFiles/MolClockAllRoots.bf lib/hyphy/TemplateBatchFiles/MolecularClock.bf @@ -228,31 +153,25 @@ 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/ProteinGTRFit.bf +lib/hyphy/TemplateBatchFiles/ProteinAnalyses/ProteinGTRFit_helper.ibf lib/hyphy/TemplateBatchFiles/ProteinAnalyses/README_relative_prot_rates.md +lib/hyphy/TemplateBatchFiles/ProteinAnalyses/plusF_helper.ibf lib/hyphy/TemplateBatchFiles/ProteinAnalyses/relative_prot_rates.bf -lib/hyphy/TemplateBatchFiles/QuickSelectionDetection-MEME-internal.bf -lib/hyphy/TemplateBatchFiles/Deprecated/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/SM-2019.bf +lib/hyphy/TemplateBatchFiles/Samplers/lhc-ErrorEst.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-ErrorEst.ibf lib/hyphy/TemplateBatchFiles/Samplers/srs.ibf lib/hyphy/TemplateBatchFiles/SandNSAmbigs.bf lib/hyphy/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf @@ -261,47 +180,29 @@ lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FADE.bf lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FEL-contrast.bf lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FEL.bf lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf +lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FitMultiModel.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/Simulators/BUSTED.bf -lib/hyphy/TemplateBatchFiles/SelectionAnalyses/Simulators/FADE.bf -lib/hyphy/TemplateBatchFiles/SelectionAnalyses/aBSREL-NS.bf +lib/hyphy/TemplateBatchFiles/SelectionAnalyses/SingleOmega.bf lib/hyphy/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/grid_compute.ibf 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/SelectionAnalyses/testers/FitModel.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 @@ -442,12 +343,10 @@ lib/hyphy/TemplateBatchFiles/Utility/ReadDelimitedFile 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 @@ -455,11 +354,8 @@ lib/hyphy/TemplateBatchFiles/branchSwappingFunctions.b 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 @@ -477,7 +373,9 @@ 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/function-loader.bf lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf +lib/hyphy/TemplateBatchFiles/libv3/models/DNA/GTR-MutSel.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 @@ -488,6 +386,7 @@ 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/codon/MG_REV_MH.bf +lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV_TRIP.bf lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf lib/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf @@ -507,6 +406,7 @@ 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/bayesgraph.ibf +lib/hyphy/TemplateBatchFiles/libv3/tasks/distances.bf lib/hyphy/TemplateBatchFiles/libv3/tasks/estimators.bf lib/hyphy/TemplateBatchFiles/libv3/tasks/genetic_code.bf lib/hyphy/TemplateBatchFiles/libv3/tasks/mpi.bf @@ -515,19 +415,7 @@ 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/posteriors.ibf lib/hyphy/TemplateBatchFiles/qndhelper1.ibf lib/hyphy/TemplateBatchFiles/qndhelper1_mf.ibf lib/hyphy/TemplateBatchFiles/qndhelper2.ibf @@ -536,60 +424,10 @@ lib/hyphy/TemplateBatchFiles/qndhelper3.ibf lib/hyphy/TemplateBatchFiles/qndhelper4.ibf lib/hyphy/TemplateBatchFiles/queryTree.bf lib/hyphy/TemplateBatchFiles/readIndexFile.bf +lib/hyphy/TemplateBatchFiles/relative_nucleotide_rates.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