├── .gitignore ├── .travis.yml ├── Dockerfile ├── INSTALL.sh ├── LICENSE ├── README.md ├── docs ├── citation.rst ├── conf.py ├── img │ └── logo.png ├── index.rst ├── install │ ├── conda.rst │ ├── docker.rst │ └── web-interface.rst ├── introduction │ ├── introduction.rst │ └── runphame.rst └── usage │ └── cases.rst ├── lib ├── PhaME.pm ├── fastq_utility.pm └── misc_funcs.pm ├── phame.ctl ├── src ├── CanSNPs.pl ├── ParseTree.pl ├── SNP_INDEL_count.pl ├── SNP_analysis.pl ├── buildSNPDB.pl ├── catAlign.pl ├── checkNUCmer.pl ├── extractGenes.pl ├── get_repeat_coords.pl ├── pal2nal.pl ├── parallel_run.pl ├── parseGapsNUCmer.pl ├── parseSitePAML.pl ├── phame ├── removeGaps.pl ├── removeRepeats.pl ├── runContigNUCmer.pl ├── runHyPhy.pl ├── runNUCmer.pl ├── runPAML.pl ├── runReadsMapping.pl ├── runReadsToGenome.pl ├── translate.pl └── vcfutils.pl ├── test ├── TestAll.sh ├── ctl_files │ ├── ecoli.ctl │ ├── t10A_error_message.ctl │ ├── t10B_error_message.ctl │ ├── t10_ebola_sreads_preads.ctl │ ├── t11_flu_test_coverage_threshold.ctl │ ├── t12_ebola_comp_contigs_pread_sread.ctl │ ├── t13_realignment.ctl │ ├── t14_secondtime.ctl │ ├── t15_ebola_complete_contigs_sread_pread.ctl │ ├── t16_ebola_comp_contigs_sread.ctl │ ├── t1_ebola_preads.ctl │ ├── t2_ebola_sreads.ctl │ ├── t3_ebola_contigs.ctl │ ├── t4_ebola_complete.ctl │ ├── t5_ebola_cmp_ctgs.ctl │ ├── t6_ebola_cmp_sreads.ctl │ ├── t7_ebola_cmp_preads.ctl │ ├── t8_ebola_ctg_sreads.ctl │ └── t9_ebola_ctg_preads.ctl ├── data │ ├── ebola_contigs │ │ ├── ebola.contigs │ │ ├── ebola_1gene.contig │ │ └── ebola_partial_genome.contig │ ├── ebola_reads │ │ ├── SRR3359589_R1.fastq │ │ ├── SRR3359589_R2.fastq │ │ ├── SRR3359589_single.fastq │ │ ├── SRR5528819_R1.fastq │ │ └── SRR5528819_R2.fastq │ ├── ebola_ref │ │ ├── KJ660347.ref_genome.fasta │ │ ├── KJ660347.ref_genome.gff │ │ ├── ZEBOV_2002_Ilembe.fna │ │ ├── ZEBOV_2007_0Luebo.fna │ │ ├── ZEBOV_2007_1Luebo.fna │ │ ├── ZEBOV_2007_23Luebo.fna │ │ ├── ZEBOV_2007_43Luebo.fna │ │ ├── ZEBOV_2007_4Luebo.fna │ │ ├── ZEBOV_2007_5Luebo.fna │ │ └── ZEBOV_2007_9Luebo.fna │ └── flu_ref │ │ ├── gb_CY129546_21-1721_Organism_Influenza.fa │ │ ├── gb_CY129910_21-1721_Organism_Influenza.fa │ │ ├── gb_CY129918_21-1721_Organism_Influenza.fa │ │ ├── gb_CY129926_14-1714_Organism_Influenza.fa │ │ ├── gb_CY129934_21-1721_Organism_Influenza.fa │ │ ├── gb_CY129942_21-1721_Organism_Influenza.fa │ │ ├── gb_CY176570_21-1721_Organism_Influenza.fa │ │ ├── gb_CY176578_21-1721_Organism_Influenza.fa │ │ ├── gb_CY176586_18-1718_Organism_Influenza.fa │ │ ├── gb_KF041867_33-1651_Organism_Influenza.fa │ │ ├── gb_KT889256_1-1701_Organism_Influenza.fa │ │ ├── gb_KX088384_1-1701_Organism_Influenza.fa │ │ ├── gb_KX097043_1-1701_Organism_Influenza.fa │ │ ├── gb_KX097044_1-1701_Organism_Influenza.fa │ │ ├── gb_KX097045_1-1701_Organism_Influenza.fa │ │ ├── gb_KX097046_1-1701_Organism_Influenza.fa │ │ ├── gb_KX097047_1-1701_Organism_Influenza.fa │ │ ├── gb_KX097048_1-1701_Organism_Influenza.fa │ │ ├── gb_KX214547_1-1701_Organism_Influenza.fa │ │ ├── gb_KX214548_1-1701_Organism_Influenza.fa │ │ ├── gb_KX214551_1-1701_Organism_Influenza.fa │ │ ├── gb_KX214552_1-1701_Organism_Influenza.fa │ │ ├── gb_KX214555_1-1687_Organism_Influenza.fa │ │ ├── gb_KX214556_1-1686_Organism_Influenza.fa │ │ ├── gb_KX214557_1-1662_Organism_Influenza.fa │ │ └── gb_KX214559_1-1381_Organism_Influenza.fa ├── testPickRefGenome.t ├── test_completeNUCmer.t ├── test_filter_genomes.t ├── test_read_directory.t └── truth │ ├── t1_all_snp_alignment.fna │ ├── t1_summaryStatistics.txt │ ├── t2_all_snp_alignment.fna │ ├── t2_summaryStatistics.txt │ ├── t3_all_snp_alignment.fna │ ├── t3_summaryStatistics.txt │ ├── t4_all_snp_alignment.fna │ ├── t5_all_snp_alignment.fna │ ├── t6_all_snp_alignment.fna │ ├── t7_all_snp_alignment.fna │ └── t8_all_snp_alignment.fna └── thirdParty └── hyphy_batch_files └── TemplateBatchFiles ├── 2RatesAnalyses ├── GY94.mdl ├── MG94GY94xREV_PARRIS_syn3.mdl ├── MG94xREV.mdl ├── MG94xREVxBivariate.mdl ├── MG94xREVxBivariate_Multirate.mdl ├── PARRIS_M1.def ├── PARRIS_M2.def ├── PARRIS_M3.def ├── PARRIS_syn3.def ├── PARRIS_synvar.def ├── discreteGenerator.bf ├── discreteGeneratorNoPS.bf ├── gamma1.def ├── gamma2+Inv.def └── gamma2.def ├── 454.bf ├── AAModelComparison.bf ├── AddABias.ibf ├── AnalyzeCodonData.bf ├── AnalyzeCodonDataMPI.bf ├── AnalyzeDiNucData.bf ├── AnalyzeNucDataFreq.bf ├── AnalyzeNucDataFreq2.bf ├── AnalyzeNucProtData.bf ├── AnalyzeNucProtData2.bf ├── BGM.bf ├── BS2007.bf ├── BUSTED-SRV.bf ├── BivariateCodonRateAnalysis.bf ├── BranchClassDNDS.bf ├── BranchSiteREL.bf ├── BranchSiteRELMultiModel.bf ├── BranchSwap.bf ├── CleanGaps.bf ├── CleanStopCodons.bf ├── ClusterAnalysis.bf ├── ClusterByDistanceRange.bf ├── CodonBivariateRateProcessor.bf ├── CodonModelCompare.bf ├── CodonToProtein.bf ├── CodonUsageBias.bf ├── CompareSelectivePressure.bf ├── CompareSelectivePressureIVL.bf ├── ConvertDataFile.bf ├── DatedTipsMolecularClock.bf ├── DirectionalREL.bf ├── DirectionalREL_MF.bf ├── DistanceMatrix.bf ├── DistanceMatrix_Splits.bf ├── Distances ├── CodonTools.def ├── CodonTools2.def ├── CodonToolsMain.def ├── JC69 ├── K2P ├── K2P_RV ├── Modified_Nei_Gojobori ├── Nei_Gojobori ├── PC ├── PC_MH ├── PC_RV ├── T3P ├── TN84 ├── TN93 ├── TN93_RV ├── Unaligned_LZ ├── Unaligned_LZ_FR ├── p_Distance ├── p_Distance_aa ├── p_Distance_binary └── p_Distance_codon ├── F_ST.bf ├── FitnessAAModels.bf ├── GADatedClock.bf ├── GADatedClock.ibf ├── GADatedClockProcessor.bf ├── GADatedClockProcessorM.bf ├── GARD.bf ├── GARDProcessor.bf ├── GARD_GA_CHC.ibf ├── GARecomb.bf ├── GA_CHC.ibf ├── GA_CHC_Binary.ibf ├── GA_CHC_kernel.ibf ├── GUI └── crayolaColors.def ├── Gateaux.bf ├── Gateaux2.bf ├── GateauxMR.bf ├── KHTest.bf ├── Kernel_PCA.bf ├── Kernel_k_means.bf ├── Kernel_support.ibf ├── LEISR.bf ├── LHT.bf ├── LRTRecombTest.bf ├── LZ_Complexity.bf ├── LocalBranchSiteTest.bf ├── LocalMolClock.bf ├── MEDS.bf ├── MEME_mf.bf ├── MFPSreader.def ├── MFPositiveSelection.bf ├── MFPositiveSelectionPooled.bf ├── MGvsGY.bf ├── MaxChi2.bf ├── MergeSequences.bf ├── MergeSites.bf ├── ModelSelectorAAProcessor.bf ├── ModelSelectorBranch.bf ├── ModelSelectorCodon.bf ├── ModelSelectorCodon.ibf ├── ModelSelectorCodonProcessor.bf ├── ModelSelectorRNA.bf ├── ModelSelectorRNA_1.bf ├── ModelTest.bf ├── MolClockAllRoots.bf ├── MolecularClock.bf ├── NeighborJoining.bf ├── NielsenYang.bf ├── NucModelCompare.bf ├── PARRIS.bf ├── PairwiseRelativeRate.bf ├── PairwiseRelativeRatio.bf ├── PairwiseSiteDiversity.bf ├── PartitionDataFile.bf ├── PartitionRateComparison.bf ├── Phylohandbook.bf ├── Plato.bf ├── PositiveSelectionLI.bf ├── ProteinAnalyses ├── README_relative_prot_rates.md └── relative_prot_rates.bf ├── QuickSelectionDetection-MEME-internal.bf ├── QuickSelectionDetection.bf ├── QuickSelectionDetectionMF.bf ├── RateClassCounter.bf ├── ReduceDataSetMatrix.bf ├── RelativeRate.bf ├── RelativeRateL.bf ├── RelativeRatio.bf ├── SGASimProcessor.bf ├── SGEmulator.bf ├── SGEmulator_MF.bf ├── SGIvL.bf ├── SSRatesTest.bf ├── SampleProcessor.bf ├── Samplers ├── lhc.bf ├── lhc_supp.ibf ├── sir.bf └── srs.ibf ├── SandNSAmbigs.bf ├── SelectionAnalyses ├── BUSTED.bf ├── BranchSiteREL.bf ├── FEL-contrast.bf ├── FEL.bf ├── FUBAR.bf ├── MEME.bf ├── RELAX-Groups.bf ├── RELAX-SRV.bf ├── RELAX.bf ├── SLAC.bf ├── aBSREL.bf └── modules │ ├── io_functions.ibf │ ├── selection_lib.ibf │ └── shared-load-file.bf ├── SelectionLRT.bf ├── SeqAlignShared.ibf ├── SeqAlignment.bf ├── SeqAlignmentCodon.bf ├── SeqAlignmentCodonShared.ibf ├── SeqAlignmentNuc.bf ├── SeqAlignmentNucShared.ibf ├── SeqAlignmentProt.bf ├── SeqAlignmentTop75.bf ├── SequentialAddition.bf ├── SequentialAddition.ibf ├── SimilarityPlot.bf ├── SimmondsAI.bf ├── SimpleMutationCounter.bf ├── SingleBreakpointRecomb-2.bf ├── SingleBreakpointRecomb.bf ├── SiteRates.bf ├── SiteRates2.bf ├── SlatkinMaddison-2parts.bf ├── SlatkinMaddison.bf ├── SlidingNucWindow.bf ├── SlidingWindowAnalysis.bf ├── SplitSequencesByPattern.bf ├── StarDecomposition.bf ├── StrandGRMTest.bf ├── StripStopCodons.bf ├── SubtreeSelectionComparison.bf ├── TemplateModels ├── 190 ├── BranchSiteTemplate.mdl ├── CF3x4.bf ├── Custom_AA.mdl ├── Custom_AA_empirical.mdl ├── Dayhoff.mdl ├── Dayhoff_F.mdl ├── Default ├── ECM+F+omega.mdl ├── ECM+F.mdl ├── ECM+F3x4.mdl ├── ECM+MLFREQS.mdl ├── ECM.mdl ├── EIAA.mdl ├── EIAAFreq.mdl ├── EX.dat ├── EX.mdl ├── EmpiricalAA │ ├── BLOSUM62 │ ├── Dayhoff │ ├── H5N1 │ ├── HIVBetween │ ├── HIVWithin │ ├── IAV │ ├── JTT │ ├── LCAP │ ├── LG │ ├── MtArt │ ├── VT │ ├── WAG │ ├── cpREV │ ├── modellist.ibf │ ├── mtMAM │ ├── mtREV24 │ └── rtREV ├── EmpiricalCodon │ ├── KHG_ECM │ └── KHG_ECMu ├── F81.mdl ├── F81_binary.mdl ├── F84.mdl ├── F84P.mdl ├── GRM.mdl ├── GY94.ibf ├── GY94.mdl ├── GY94customF3x4.mdl ├── GY94w9.mdl ├── HIVbetween+F.mdl ├── HIVbetween.ibf ├── HIVbetween.mdl ├── HIVwithin+F.mdl ├── HIVwithin.ibf ├── HIVwithin.mdl ├── HKY85.mdl ├── JC69.mdl ├── JC69_binary.mdl ├── Jones.mdl ├── Jones_F.mdl ├── K2P.mdl ├── K3ST.mdl ├── LCAP.mdl ├── MEC.mdl ├── MG94.mdl ├── MG94custom.mdl ├── MG94customCF3x4.mdl ├── MG94customF1x4.mdl ├── MG94customFreqs.mdl ├── MG94wAA.mdl ├── MG94wAAF61.mdl ├── MG94wAAF61multiple.mdl ├── MG94wAAFreqs.mdl ├── MG94wAAUserFreqs.mdl ├── MG94wEX.mdl ├── MG94with9freqs.mdl ├── MG94x2.mdl ├── MGFreqsEstimator.ibf ├── MGwAA.ibf ├── MGwEX.ibf ├── NRM+Freqs.mdl ├── NRM.mdl ├── PCH ├── RNA16.mdl ├── RNA16A ├── RNA16SvH.mdl ├── RNAEqualInput ├── RNAF81 ├── RNAMuse95.mdl ├── RNAREV ├── RNAREV_1 ├── S4 ├── STGRM.mdl ├── TrN.mdl ├── UniversalCode.def ├── WAG.mdl ├── WAG_F.mdl ├── Yang2000Distributions.def ├── chooseGeneticCode.def ├── custm4x4.mdl ├── defineGamma.mdl ├── defineHM.mdl ├── fitness.mdl ├── modelParameters.mdl ├── modelParameters2.mdl ├── modelParameters3.mdl ├── modelParameters4.mdl ├── modelParameters5.mdl ├── models.lst ├── mtMAM.mdl ├── mtMAM_F.mdl ├── mtREV.mdl ├── mtREV_24.mdl ├── mtREV_24_F.mdl ├── reducedREV.mdl ├── rtREV.mdl └── rtREV_F.mdl ├── TestBranchDNDS.bf ├── TestClade.bf ├── TestCladeMeans.bf ├── TopologySearch.bf ├── TopologySearchConstrained.bf ├── TreeCorrelationCoefficients.bf ├── TreeTools.ibf ├── UpperBound.bf ├── Utility ├── AncestralMapper.bf ├── BranchLengthFitters.bf ├── CoalescentPostProcessor.bf ├── CodonTools.bf ├── DBTools.ibf ├── DescriptiveStatistics.bf ├── GrabBag.bf ├── HXB2Mapper.bf ├── LocalMGREV.bf ├── LocalMGREVMLFreqs.bf ├── MPITools.bf ├── NJ.bf ├── PS_Plotters.bf ├── PostScript.bf ├── ProbabilityDistributions.bf ├── ReadDelimitedFiles.bf ├── TreeFunctions.bf └── WriteDelimitedFiles.bf ├── WANC.bf ├── WebUpdate.bf ├── YangNielsenBranchSite2005.bf ├── _BMS_Aux.ibf ├── _CMS_Aux.ibf ├── _MFReader_.ibf ├── _MSCOneStep.ibf ├── _tipDater.ibf ├── bayesgraph.ibf ├── binomial.ibf ├── branchSwappingFunctions.bf ├── categoryEcho.bf ├── chooseDistanceFormula.def ├── dNdSBivariateRateAnalysis.bf ├── dNdSBivariateRateAnalysis_CompareDS.bf ├── dNdSDistributionComparison.bf ├── dNdSDistributionComparisonPartitions.bf ├── dNdSRateAnalysis.bf ├── dNdSRateAnalysis_MF.bf ├── dNdSResultProcessor.bf ├── dSdNTreeTools.ibf ├── distanceMethodNPBootstrap.bf ├── distanceRMethodNPBootstrap.bf ├── doNNISwap.bf ├── doSPRSwap.bf ├── files.lst ├── globalChecker.ibf ├── heuristicMethodNPBootstrap.bf ├── last.date ├── libv3 ├── IOFunctions.bf ├── UtilityFunctions.bf ├── all-terms.bf ├── convenience │ ├── math.bf │ ├── matrix.bf │ ├── random.bf │ └── regexp.bf ├── models │ ├── DNA.bf │ ├── DNA │ │ ├── GTR.bf │ │ ├── HKY85.bf │ │ └── JC69.bf │ ├── binary.bf │ ├── binary │ │ └── charbinary.bf │ ├── codon.bf │ ├── codon │ │ ├── BS_REL.bf │ │ └── MG_REV.bf │ ├── frequencies.bf │ ├── model_functions.bf │ ├── parameters.bf │ ├── protein.bf │ ├── protein │ │ ├── REV.bf │ │ ├── empirical.bf │ │ ├── matrices │ │ │ ├── HIV.ibf │ │ │ ├── JC69.ibf │ │ │ ├── JTT.ibf │ │ │ ├── LG.ibf │ │ │ ├── WAG.ibf │ │ │ ├── gcpREV.ibf │ │ │ └── mt.ibf │ │ └── matrix2dict_aux.bf │ └── rate_variation.bf 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