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Port details
hyphy Hypothesis testing using Phylogenies
2.3.14.16 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 11 May 2018 00:05:33
License: MIT
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/
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (599 items)
  1. /usr/local/share/licenses/hyphy-2.3.14.16/catalog.mk
  2. /usr/local/share/licenses/hyphy-2.3.14.16/LICENSE
  3. /usr/local/share/licenses/hyphy-2.3.14.16/MIT
  4. bin/HYPHYMP
  5. lib/hyphy/ChartAddIns/Approximate_CDF
  6. lib/hyphy/ChartAddIns/Column Operations
  7. lib/hyphy/ChartAddIns/Complex Select Cells By Value
  8. lib/hyphy/ChartAddIns/Contigency Table
  9. lib/hyphy/ChartAddIns/Covariance
  10. lib/hyphy/ChartAddIns/DBAddIns/DescriptiveStats.bf
  11. lib/hyphy/ChartAddIns/DBAddIns/FromSQLFlatFile.bf
  12. lib/hyphy/ChartAddIns/DBAddIns/HY_DBW_TemplateList
  13. lib/hyphy/ChartAddIns/DBAddIns/ToChartWindow.bf
  14. lib/hyphy/ChartAddIns/DBAddIns/ToConsole.bf
  15. lib/hyphy/ChartAddIns/DBAddIns/ToFastaFile.bf
  16. lib/hyphy/ChartAddIns/DBAddIns/ToFastaFileFromPandit.bf
  17. lib/hyphy/ChartAddIns/DBAddIns/ToFrontierFastaFile.bf
  18. lib/hyphy/ChartAddIns/DBAddIns/ToSQLFlatFile.bf
  19. lib/hyphy/ChartAddIns/DBAddIns/ToTabFile.bf
  20. lib/hyphy/ChartAddIns/Descriptive Statistics
  21. lib/hyphy/ChartAddIns/Distribution Moments
  22. lib/hyphy/ChartAddIns/DistributionAddIns/Event Posteriors
  23. lib/hyphy/ChartAddIns/DistributionAddIns/Includes/posteriors.ibf
  24. lib/hyphy/ChartAddIns/DistributionAddIns/Most Likely Class Assignment
  25. lib/hyphy/ChartAddIns/DistributionAddIns/Posterior Distribution
  26. lib/hyphy/ChartAddIns/DistributionAddIns/Posterior Moments
  27. lib/hyphy/ChartAddIns/DistributionAddIns/Prior Moments
  28. lib/hyphy/ChartAddIns/Gaussian Penalty Clustering
  29. lib/hyphy/ChartAddIns/Goodness of Fit
  30. lib/hyphy/ChartAddIns/Histogram
  31. lib/hyphy/ChartAddIns/K-Mean Clustering
  32. lib/hyphy/ChartAddIns/KH Resampler
  33. lib/hyphy/ChartAddIns/Linear Fit
  34. lib/hyphy/ChartAddIns/Mean Profile Plot
  35. lib/hyphy/ChartAddIns/Median Profile Plot
  36. lib/hyphy/ChartAddIns/Poisson Mixture Fit
  37. lib/hyphy/ChartAddIns/Populate Cells
  38. lib/hyphy/ChartAddIns/Profile Mean Clustering
  39. lib/hyphy/ChartAddIns/Running Sum
  40. lib/hyphy/ChartAddIns/Samplers/lhc.bf
  41. lib/hyphy/ChartAddIns/Samplers/sir.bf
  42. lib/hyphy/ChartAddIns/Samplers/srs.ibf
  43. lib/hyphy/ChartAddIns/Select Cells By Index
  44. lib/hyphy/ChartAddIns/Select Cells By Value
  45. lib/hyphy/ChartAddIns/SingleColumn
  46. lib/hyphy/ChartAddIns/Sort
  47. lib/hyphy/DatapanelAddIns/Character Plot
  48. lib/hyphy/DatapanelAddIns/Character Plot Two
  49. lib/hyphy/DatapanelAddIns/Compare Subsets
  50. lib/hyphy/DatapanelAddIns/Sequence Plot
  51. lib/hyphy/DatapanelAddIns/TBD/Character Plot By Sequence
  52. lib/hyphy/DatapanelAddIns/ibfs/char_colors.def
  53. lib/hyphy/GeneticCodes/Alt_Yeast_Nuclear.cod
  54. lib/hyphy/GeneticCodes/Ascidian_mtDNA.cod
  55. lib/hyphy/GeneticCodes/Blepharisma_Nuclear.cod
  56. lib/hyphy/GeneticCodes/Ciliate.cod
  57. lib/hyphy/GeneticCodes/Echinoderm_mtDNA.cod
  58. lib/hyphy/GeneticCodes/Euplotid_Nuclear.cod
  59. lib/hyphy/GeneticCodes/Flatworm_mtDNA.cod
  60. lib/hyphy/GeneticCodes/Invertebrate_mtDNA.cod
  61. lib/hyphy/GeneticCodes/Mold_mtDNA.cod
  62. lib/hyphy/GeneticCodes/Thraustochytrium_mtDNA.cod
  63. lib/hyphy/GeneticCodes/Vertebratemtdna.cod
  64. lib/hyphy/GeneticCodes/Yeast_mtDNA.cod
  65. lib/hyphy/SubstitutionClasses/AAEFV/Equal
  66. lib/hyphy/SubstitutionClasses/AAEFV/Estimated
  67. lib/hyphy/SubstitutionClasses/AAEFV/Observed In Data Set
  68. lib/hyphy/SubstitutionClasses/AAEFV/Observed In Partition
  69. lib/hyphy/SubstitutionClasses/CodonEFV/Equal
  70. lib/hyphy/SubstitutionClasses/CodonEFV/Observed Codon
  71. lib/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 3 params.
  72. lib/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 9 params.
  73. lib/hyphy/SubstitutionClasses/Heterogeneity/2 Bin Discrete
  74. lib/hyphy/SubstitutionClasses/Heterogeneity/Beta
  75. lib/hyphy/SubstitutionClasses/Heterogeneity/Beta-Gamma
  76. lib/hyphy/SubstitutionClasses/Heterogeneity/General Discrete
  77. lib/hyphy/SubstitutionClasses/Heterogeneity/Half Normal
  78. lib/hyphy/SubstitutionClasses/Heterogeneity/Lognormal
  79. lib/hyphy/SubstitutionClasses/NucEFV/Equal
  80. lib/hyphy/SubstitutionClasses/NucEFV/Estimated
  81. lib/hyphy/SubstitutionClasses/NucEFV/Observed In Data Set
  82. lib/hyphy/SubstitutionClasses/NucEFV/Observed In Partition
  83. lib/hyphy/SubstitutionClasses/aa.bf
  84. lib/hyphy/SubstitutionClasses/codon.bf
  85. lib/hyphy/SubstitutionClasses/dinuc.bf
  86. lib/hyphy/SubstitutionClasses/nuc.bf
  87. lib/hyphy/SubstitutionModels/Aminoacid/Dayhoff.mdl
  88. lib/hyphy/SubstitutionModels/Aminoacid/EIAA.mdl
  89. lib/hyphy/SubstitutionModels/Aminoacid/Fitness.mdl
  90. lib/hyphy/SubstitutionModels/Aminoacid/Jones.mdl
  91. lib/hyphy/SubstitutionModels/Aminoacid/mtREV.mdl
  92. lib/hyphy/SubstitutionModels/Binary/F81.mdl
  93. lib/hyphy/SubstitutionModels/Codon/GY94_3x4.mdl
  94. lib/hyphy/SubstitutionModels/Codon/Lineage_MG94xHKY85.mdl
  95. lib/hyphy/SubstitutionModels/Codon/MG94.mdl
  96. lib/hyphy/SubstitutionModels/Codon/MG94REVOmegaCF3x4.mdl
  97. lib/hyphy/SubstitutionModels/Codon/MG94_3x4.mdl
  98. lib/hyphy/SubstitutionModels/Codon/MG94_HKY85x3_4.mdl
  99. lib/hyphy/SubstitutionModels/Codon/MG94_REV_3x4.mdl
  100. lib/hyphy/SubstitutionModels/Codon/MG94xHKY85_3x4_2Rates.mdl
  101. lib/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV.mdl
  102. lib/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV_GDD.mdl
  103. lib/hyphy/SubstitutionModels/Codon/MG94xTN93_3x4.mdl
  104. lib/hyphy/SubstitutionModels/Nucleotide/EFVEstimated.ibf
  105. lib/hyphy/SubstitutionModels/Nucleotide/F81.mdl
  106. lib/hyphy/SubstitutionModels/Nucleotide/HKY85.mdl
  107. lib/hyphy/SubstitutionModels/Nucleotide/REV.mdl
  108. lib/hyphy/SubstitutionModels/Nucleotide/REVBetaGamma.mdl
  109. lib/hyphy/SubstitutionModels/Nucleotide/TrN.mdl
  110. lib/hyphy/SubstitutionModels/User/Nucleotide/JC69
  111. lib/hyphy/SubstitutionModels/User/Nucleotide/K2P
  112. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/GY94.mdl
  113. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94GY94xREV_PARRIS_syn3.mdl
  114. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREV.mdl
  115. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate.mdl
  116. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate_Multirate.mdl
  117. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M1.def
  118. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M2.def
  119. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M3.def
  120. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_syn3.def
  121. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_synvar.def
  122. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGenerator.bf
  123. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGeneratorNoPS.bf
  124. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma1.def
  125. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2+Inv.def
  126. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2.def
  127. lib/hyphy/TemplateBatchFiles/454.bf
  128. lib/hyphy/TemplateBatchFiles/AAModelComparison.bf
  129. lib/hyphy/TemplateBatchFiles/AddABias.ibf
  130. lib/hyphy/TemplateBatchFiles/AnalyzeCodonData.bf
  131. lib/hyphy/TemplateBatchFiles/AnalyzeCodonDataMPI.bf
  132. lib/hyphy/TemplateBatchFiles/AnalyzeDiNucData.bf
  133. lib/hyphy/TemplateBatchFiles/AnalyzeNucDataFreq.bf
  134. lib/hyphy/TemplateBatchFiles/AnalyzeNucDataFreq2.bf
  135. lib/hyphy/TemplateBatchFiles/AnalyzeNucProtData.bf
  136. lib/hyphy/TemplateBatchFiles/AnalyzeNucProtData2.bf
  137. lib/hyphy/TemplateBatchFiles/BGM.bf
  138. lib/hyphy/TemplateBatchFiles/BS2007.bf
  139. lib/hyphy/TemplateBatchFiles/BUSTED-SRV.bf
  140. lib/hyphy/TemplateBatchFiles/BivariateCodonRateAnalysis.bf
  141. lib/hyphy/TemplateBatchFiles/BranchClassDNDS.bf
  142. lib/hyphy/TemplateBatchFiles/BranchSiteREL.bf
  143. lib/hyphy/TemplateBatchFiles/BranchSiteRELMultiModel.bf
  144. lib/hyphy/TemplateBatchFiles/BranchSwap.bf
  145. lib/hyphy/TemplateBatchFiles/CleanGaps.bf
  146. lib/hyphy/TemplateBatchFiles/CleanStopCodons.bf
  147. lib/hyphy/TemplateBatchFiles/ClusterAnalysis.bf
  148. lib/hyphy/TemplateBatchFiles/ClusterByDistanceRange.bf
  149. lib/hyphy/TemplateBatchFiles/CodonBivariateRateProcessor.bf
  150. lib/hyphy/TemplateBatchFiles/CodonModelCompare.bf
  151. lib/hyphy/TemplateBatchFiles/CodonToProtein.bf
  152. lib/hyphy/TemplateBatchFiles/CodonUsageBias.bf
  153. lib/hyphy/TemplateBatchFiles/CompareSelectivePressure.bf
  154. lib/hyphy/TemplateBatchFiles/CompareSelectivePressureIVL.bf
  155. lib/hyphy/TemplateBatchFiles/ConvertDataFile.bf
  156. lib/hyphy/TemplateBatchFiles/DatedTipsMolecularClock.bf
  157. lib/hyphy/TemplateBatchFiles/DirectionalREL.bf
  158. lib/hyphy/TemplateBatchFiles/DirectionalREL_MF.bf
  159. lib/hyphy/TemplateBatchFiles/DistanceMatrix.bf
  160. lib/hyphy/TemplateBatchFiles/DistanceMatrix_Splits.bf
  161. lib/hyphy/TemplateBatchFiles/Distances/CodonTools.def
  162. lib/hyphy/TemplateBatchFiles/Distances/CodonTools2.def
  163. lib/hyphy/TemplateBatchFiles/Distances/CodonToolsMain.def
  164. lib/hyphy/TemplateBatchFiles/Distances/JC69
  165. lib/hyphy/TemplateBatchFiles/Distances/K2P
  166. lib/hyphy/TemplateBatchFiles/Distances/K2P_RV
  167. lib/hyphy/TemplateBatchFiles/Distances/Modified_Nei_Gojobori
  168. lib/hyphy/TemplateBatchFiles/Distances/Nei_Gojobori
  169. lib/hyphy/TemplateBatchFiles/Distances/PC
  170. lib/hyphy/TemplateBatchFiles/Distances/PC_MH
  171. lib/hyphy/TemplateBatchFiles/Distances/PC_RV
  172. lib/hyphy/TemplateBatchFiles/Distances/T3P
  173. lib/hyphy/TemplateBatchFiles/Distances/TN84
  174. lib/hyphy/TemplateBatchFiles/Distances/TN93
  175. lib/hyphy/TemplateBatchFiles/Distances/TN93_RV
  176. lib/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ
  177. lib/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ_FR
  178. lib/hyphy/TemplateBatchFiles/Distances/p_Distance
  179. lib/hyphy/TemplateBatchFiles/Distances/p_Distance_aa
  180. lib/hyphy/TemplateBatchFiles/Distances/p_Distance_binary
  181. lib/hyphy/TemplateBatchFiles/Distances/p_Distance_codon
  182. lib/hyphy/TemplateBatchFiles/F_ST.bf
  183. lib/hyphy/TemplateBatchFiles/FitnessAAModels.bf
  184. lib/hyphy/TemplateBatchFiles/GADatedClock.bf
  185. lib/hyphy/TemplateBatchFiles/GADatedClock.ibf
  186. lib/hyphy/TemplateBatchFiles/GADatedClockProcessor.bf
  187. lib/hyphy/TemplateBatchFiles/GADatedClockProcessorM.bf
  188. lib/hyphy/TemplateBatchFiles/GARD.bf
  189. lib/hyphy/TemplateBatchFiles/GARDProcessor.bf
  190. lib/hyphy/TemplateBatchFiles/GARD_GA_CHC.ibf
  191. lib/hyphy/TemplateBatchFiles/GARecomb.bf
  192. lib/hyphy/TemplateBatchFiles/GA_CHC.ibf
  193. lib/hyphy/TemplateBatchFiles/GA_CHC_Binary.ibf
  194. lib/hyphy/TemplateBatchFiles/GA_CHC_kernel.ibf
  195. lib/hyphy/TemplateBatchFiles/GUI/crayolaColors.def
  196. lib/hyphy/TemplateBatchFiles/Gateaux.bf
  197. lib/hyphy/TemplateBatchFiles/Gateaux2.bf
  198. lib/hyphy/TemplateBatchFiles/GateauxMR.bf
  199. lib/hyphy/TemplateBatchFiles/KHTest.bf
  200. lib/hyphy/TemplateBatchFiles/Kernel_PCA.bf
  201. lib/hyphy/TemplateBatchFiles/Kernel_k_means.bf
  202. lib/hyphy/TemplateBatchFiles/Kernel_support.ibf
  203. lib/hyphy/TemplateBatchFiles/LEISR.bf
  204. lib/hyphy/TemplateBatchFiles/LHT.bf
  205. lib/hyphy/TemplateBatchFiles/LRTRecombTest.bf
  206. lib/hyphy/TemplateBatchFiles/LZ_Complexity.bf
  207. lib/hyphy/TemplateBatchFiles/LocalBranchSiteTest.bf
  208. lib/hyphy/TemplateBatchFiles/LocalMolClock.bf
  209. lib/hyphy/TemplateBatchFiles/MEDS.bf
  210. lib/hyphy/TemplateBatchFiles/MEME_mf.bf
  211. lib/hyphy/TemplateBatchFiles/MFPSreader.def
  212. lib/hyphy/TemplateBatchFiles/MFPositiveSelection.bf
  213. lib/hyphy/TemplateBatchFiles/MFPositiveSelectionPooled.bf
  214. lib/hyphy/TemplateBatchFiles/MGvsGY.bf
  215. lib/hyphy/TemplateBatchFiles/MaxChi2.bf
  216. lib/hyphy/TemplateBatchFiles/MergeSequences.bf
  217. lib/hyphy/TemplateBatchFiles/MergeSites.bf
  218. lib/hyphy/TemplateBatchFiles/ModelSelectorAAProcessor.bf
  219. lib/hyphy/TemplateBatchFiles/ModelSelectorBranch.bf
  220. lib/hyphy/TemplateBatchFiles/ModelSelectorCodon.bf
  221. lib/hyphy/TemplateBatchFiles/ModelSelectorCodon.ibf
  222. lib/hyphy/TemplateBatchFiles/ModelSelectorCodonProcessor.bf
  223. lib/hyphy/TemplateBatchFiles/ModelSelectorRNA.bf
  224. lib/hyphy/TemplateBatchFiles/ModelSelectorRNA_1.bf
  225. lib/hyphy/TemplateBatchFiles/ModelTest.bf
  226. lib/hyphy/TemplateBatchFiles/MolClockAllRoots.bf
  227. lib/hyphy/TemplateBatchFiles/MolecularClock.bf
  228. lib/hyphy/TemplateBatchFiles/NeighborJoining.bf
  229. lib/hyphy/TemplateBatchFiles/NielsenYang.bf
  230. lib/hyphy/TemplateBatchFiles/NucModelCompare.bf
  231. lib/hyphy/TemplateBatchFiles/PARRIS.bf
  232. lib/hyphy/TemplateBatchFiles/PairwiseRelativeRate.bf
  233. lib/hyphy/TemplateBatchFiles/PairwiseRelativeRatio.bf
  234. lib/hyphy/TemplateBatchFiles/PairwiseSiteDiversity.bf
  235. lib/hyphy/TemplateBatchFiles/PartitionDataFile.bf
  236. lib/hyphy/TemplateBatchFiles/PartitionRateComparison.bf
  237. lib/hyphy/TemplateBatchFiles/Phylohandbook.bf
  238. lib/hyphy/TemplateBatchFiles/Plato.bf
  239. lib/hyphy/TemplateBatchFiles/PositiveSelectionLI.bf
  240. lib/hyphy/TemplateBatchFiles/ProteinAnalyses/README_relative_prot_rates.md
  241. lib/hyphy/TemplateBatchFiles/ProteinAnalyses/relative_prot_rates.bf
  242. lib/hyphy/TemplateBatchFiles/QuickSelectionDetection-MEME-internal.bf
  243. lib/hyphy/TemplateBatchFiles/Deprecated/QuickSelectionDetection.bf
  244. lib/hyphy/TemplateBatchFiles/QuickSelectionDetectionMF.bf
  245. lib/hyphy/TemplateBatchFiles/RateClassCounter.bf
  246. lib/hyphy/TemplateBatchFiles/ReduceDataSetMatrix.bf
  247. lib/hyphy/TemplateBatchFiles/RelativeRate.bf
  248. lib/hyphy/TemplateBatchFiles/RelativeRateL.bf
  249. lib/hyphy/TemplateBatchFiles/RelativeRatio.bf
  250. lib/hyphy/TemplateBatchFiles/SGASimProcessor.bf
  251. lib/hyphy/TemplateBatchFiles/SGEmulator.bf
  252. lib/hyphy/TemplateBatchFiles/SGEmulator_MF.bf
  253. lib/hyphy/TemplateBatchFiles/SGIvL.bf
  254. lib/hyphy/TemplateBatchFiles/SSRatesTest.bf
  255. lib/hyphy/TemplateBatchFiles/SampleProcessor.bf
  256. lib/hyphy/TemplateBatchFiles/Samplers/lhc.bf
  257. lib/hyphy/TemplateBatchFiles/Samplers/lhc_supp.ibf
  258. lib/hyphy/TemplateBatchFiles/Samplers/sir.bf
  259. lib/hyphy/TemplateBatchFiles/Samplers/srs.ibf
  260. lib/hyphy/TemplateBatchFiles/SandNSAmbigs.bf
  261. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf
  262. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/BranchSiteREL.bf
  263. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FADE.bf
  264. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FEL-contrast.bf
  265. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FEL.bf
  266. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf
  267. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/MEME.bf
  268. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX-Groups.bf
  269. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX-SRV.bf
  270. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX.bf
  271. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/SLAC.bf
  272. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/Simulators/BUSTED.bf
  273. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/Simulators/FADE.bf
  274. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/aBSREL-NS.bf
  275. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf
  276. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/grid_compute.ibf
  277. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf
  278. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf
  279. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf
  280. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/testers/FitModel.bf
  281. lib/hyphy/TemplateBatchFiles/SelectionLRT.bf
  282. lib/hyphy/TemplateBatchFiles/SeqAlignShared.ibf
  283. lib/hyphy/TemplateBatchFiles/SeqAlignment.bf
  284. lib/hyphy/TemplateBatchFiles/SeqAlignmentCodon.bf
  285. lib/hyphy/TemplateBatchFiles/SeqAlignmentCodonShared.ibf
  286. lib/hyphy/TemplateBatchFiles/SeqAlignmentNuc.bf
  287. lib/hyphy/TemplateBatchFiles/SeqAlignmentNucShared.ibf
  288. lib/hyphy/TemplateBatchFiles/SeqAlignmentProt.bf
  289. lib/hyphy/TemplateBatchFiles/SeqAlignmentTop75.bf
  290. lib/hyphy/TemplateBatchFiles/SequentialAddition.bf
  291. lib/hyphy/TemplateBatchFiles/SequentialAddition.ibf
  292. lib/hyphy/TemplateBatchFiles/SimilarityPlot.bf
  293. lib/hyphy/TemplateBatchFiles/SimmondsAI.bf
  294. lib/hyphy/TemplateBatchFiles/SimpleMutationCounter.bf
  295. lib/hyphy/TemplateBatchFiles/SingleBreakpointRecomb-2.bf
  296. lib/hyphy/TemplateBatchFiles/SingleBreakpointRecomb.bf
  297. lib/hyphy/TemplateBatchFiles/SiteRates.bf
  298. lib/hyphy/TemplateBatchFiles/SiteRates2.bf
  299. lib/hyphy/TemplateBatchFiles/SlatkinMaddison-2parts.bf
  300. lib/hyphy/TemplateBatchFiles/SlatkinMaddison.bf
  301. lib/hyphy/TemplateBatchFiles/SlidingNucWindow.bf
  302. lib/hyphy/TemplateBatchFiles/SlidingWindowAnalysis.bf
  303. lib/hyphy/TemplateBatchFiles/SplitSequencesByPattern.bf
  304. lib/hyphy/TemplateBatchFiles/StarDecomposition.bf
  305. lib/hyphy/TemplateBatchFiles/StrandGRMTest.bf
  306. lib/hyphy/TemplateBatchFiles/StripStopCodons.bf
  307. lib/hyphy/TemplateBatchFiles/SubtreeSelectionComparison.bf
  308. lib/hyphy/TemplateBatchFiles/TemplateModels/190
  309. lib/hyphy/TemplateBatchFiles/TemplateModels/BranchSiteTemplate.mdl
  310. lib/hyphy/TemplateBatchFiles/TemplateModels/CF3x4.bf
  311. lib/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA.mdl
  312. lib/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA_empirical.mdl
  313. lib/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff.mdl
  314. lib/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff_F.mdl
  315. lib/hyphy/TemplateBatchFiles/TemplateModels/Default
  316. lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F+omega.mdl
  317. lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F.mdl
  318. lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F3x4.mdl
  319. lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+MLFREQS.mdl
  320. lib/hyphy/TemplateBatchFiles/TemplateModels/ECM.mdl
  321. lib/hyphy/TemplateBatchFiles/TemplateModels/EIAA.mdl
  322. lib/hyphy/TemplateBatchFiles/TemplateModels/EIAAFreq.mdl
  323. lib/hyphy/TemplateBatchFiles/TemplateModels/EX.dat
  324. lib/hyphy/TemplateBatchFiles/TemplateModels/EX.mdl
  325. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/BLOSUM62
  326. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/Dayhoff
  327. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/H5N1
  328. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVBetween
  329. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVWithin
  330. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/IAV
  331. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/JTT
  332. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LCAP
  333. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LG
  334. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/MtArt
  335. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/VT
  336. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/WAG
  337. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/cpREV
  338. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/modellist.ibf
  339. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtMAM
  340. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtREV24
  341. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/rtREV
  342. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECM
  343. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECMu
  344. lib/hyphy/TemplateBatchFiles/TemplateModels/F81.mdl
  345. lib/hyphy/TemplateBatchFiles/TemplateModels/F81_binary.mdl
  346. lib/hyphy/TemplateBatchFiles/TemplateModels/F84.mdl
  347. lib/hyphy/TemplateBatchFiles/TemplateModels/F84P.mdl
  348. lib/hyphy/TemplateBatchFiles/TemplateModels/GRM.mdl
  349. lib/hyphy/TemplateBatchFiles/TemplateModels/GY94.ibf
  350. lib/hyphy/TemplateBatchFiles/TemplateModels/GY94.mdl
  351. lib/hyphy/TemplateBatchFiles/TemplateModels/GY94customF3x4.mdl
  352. lib/hyphy/TemplateBatchFiles/TemplateModels/GY94w9.mdl
  353. lib/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween+F.mdl
  354. lib/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.ibf
  355. lib/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.mdl
  356. lib/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin+F.mdl
  357. lib/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.ibf
  358. lib/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.mdl
  359. lib/hyphy/TemplateBatchFiles/TemplateModels/HKY85.mdl
  360. lib/hyphy/TemplateBatchFiles/TemplateModels/JC69.mdl
  361. lib/hyphy/TemplateBatchFiles/TemplateModels/JC69_binary.mdl
  362. lib/hyphy/TemplateBatchFiles/TemplateModels/Jones.mdl
  363. lib/hyphy/TemplateBatchFiles/TemplateModels/Jones_F.mdl
  364. lib/hyphy/TemplateBatchFiles/TemplateModels/K2P.mdl
  365. lib/hyphy/TemplateBatchFiles/TemplateModels/K3ST.mdl
  366. lib/hyphy/TemplateBatchFiles/TemplateModels/LCAP.mdl
  367. lib/hyphy/TemplateBatchFiles/TemplateModels/MEC.mdl
  368. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94.mdl
  369. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94custom.mdl
  370. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94customCF3x4.mdl
  371. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94customF1x4.mdl
  372. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94customFreqs.mdl
  373. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAA.mdl
  374. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAF61.mdl
  375. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAF61multiple.mdl
  376. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAFreqs.mdl
  377. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAUserFreqs.mdl
  378. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wEX.mdl
  379. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94with9freqs.mdl
  380. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94x2.mdl
  381. lib/hyphy/TemplateBatchFiles/TemplateModels/MGFreqsEstimator.ibf
  382. lib/hyphy/TemplateBatchFiles/TemplateModels/MGwAA.ibf
  383. lib/hyphy/TemplateBatchFiles/TemplateModels/MGwEX.ibf
  384. lib/hyphy/TemplateBatchFiles/TemplateModels/NRM+Freqs.mdl
  385. lib/hyphy/TemplateBatchFiles/TemplateModels/NRM.mdl
  386. lib/hyphy/TemplateBatchFiles/TemplateModels/PCH
  387. lib/hyphy/TemplateBatchFiles/TemplateModels/RNA16.mdl
  388. lib/hyphy/TemplateBatchFiles/TemplateModels/RNA16A
  389. lib/hyphy/TemplateBatchFiles/TemplateModels/RNA16SvH.mdl
  390. lib/hyphy/TemplateBatchFiles/TemplateModels/RNAEqualInput
  391. lib/hyphy/TemplateBatchFiles/TemplateModels/RNAF81
  392. lib/hyphy/TemplateBatchFiles/TemplateModels/RNAMuse95.mdl
  393. lib/hyphy/TemplateBatchFiles/TemplateModels/RNAREV
  394. lib/hyphy/TemplateBatchFiles/TemplateModels/RNAREV_1
  395. lib/hyphy/TemplateBatchFiles/TemplateModels/S4
  396. lib/hyphy/TemplateBatchFiles/TemplateModels/STGRM.mdl
  397. lib/hyphy/TemplateBatchFiles/TemplateModels/TrN.mdl
  398. lib/hyphy/TemplateBatchFiles/TemplateModels/UniversalCode.def
  399. lib/hyphy/TemplateBatchFiles/TemplateModels/WAG.mdl
  400. lib/hyphy/TemplateBatchFiles/TemplateModels/WAG_F.mdl
  401. lib/hyphy/TemplateBatchFiles/TemplateModels/Yang2000Distributions.def
  402. lib/hyphy/TemplateBatchFiles/TemplateModels/chooseGeneticCode.def
  403. lib/hyphy/TemplateBatchFiles/TemplateModels/custm4x4.mdl
  404. lib/hyphy/TemplateBatchFiles/TemplateModels/defineGamma.mdl
  405. lib/hyphy/TemplateBatchFiles/TemplateModels/defineHM.mdl
  406. lib/hyphy/TemplateBatchFiles/TemplateModels/fitness.mdl
  407. lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters.mdl
  408. lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters2.mdl
  409. lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters3.mdl
  410. lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters4.mdl
  411. lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters5.mdl
  412. lib/hyphy/TemplateBatchFiles/TemplateModels/models.lst
  413. lib/hyphy/TemplateBatchFiles/TemplateModels/mtMAM.mdl
  414. lib/hyphy/TemplateBatchFiles/TemplateModels/mtMAM_F.mdl
  415. lib/hyphy/TemplateBatchFiles/TemplateModels/mtREV.mdl
  416. lib/hyphy/TemplateBatchFiles/TemplateModels/mtREV_24.mdl
  417. lib/hyphy/TemplateBatchFiles/TemplateModels/mtREV_24_F.mdl
  418. lib/hyphy/TemplateBatchFiles/TemplateModels/reducedREV.mdl
  419. lib/hyphy/TemplateBatchFiles/TemplateModels/rtREV.mdl
  420. lib/hyphy/TemplateBatchFiles/TemplateModels/rtREV_F.mdl
  421. lib/hyphy/TemplateBatchFiles/TestBranchDNDS.bf
  422. lib/hyphy/TemplateBatchFiles/TestClade.bf
  423. lib/hyphy/TemplateBatchFiles/TestCladeMeans.bf
  424. lib/hyphy/TemplateBatchFiles/TopologySearch.bf
  425. lib/hyphy/TemplateBatchFiles/TopologySearchConstrained.bf
  426. lib/hyphy/TemplateBatchFiles/TreeCorrelationCoefficients.bf
  427. lib/hyphy/TemplateBatchFiles/TreeTools.ibf
  428. lib/hyphy/TemplateBatchFiles/UpperBound.bf
  429. lib/hyphy/TemplateBatchFiles/Utility/AncestralMapper.bf
  430. lib/hyphy/TemplateBatchFiles/Utility/BranchLengthFitters.bf
  431. lib/hyphy/TemplateBatchFiles/Utility/CoalescentPostProcessor.bf
  432. lib/hyphy/TemplateBatchFiles/Utility/CodonTools.bf
  433. lib/hyphy/TemplateBatchFiles/Utility/DBTools.ibf
  434. lib/hyphy/TemplateBatchFiles/Utility/DescriptiveStatistics.bf
  435. lib/hyphy/TemplateBatchFiles/Utility/GrabBag.bf
  436. lib/hyphy/TemplateBatchFiles/Utility/HXB2Mapper.bf
  437. lib/hyphy/TemplateBatchFiles/Utility/LocalMGREV.bf
  438. lib/hyphy/TemplateBatchFiles/Utility/LocalMGREVMLFreqs.bf
  439. lib/hyphy/TemplateBatchFiles/Utility/MPITools.bf
  440. lib/hyphy/TemplateBatchFiles/Utility/NJ.bf
  441. lib/hyphy/TemplateBatchFiles/Utility/PS_Plotters.bf
  442. lib/hyphy/TemplateBatchFiles/Utility/PostScript.bf
  443. lib/hyphy/TemplateBatchFiles/Utility/ProbabilityDistributions.bf
  444. lib/hyphy/TemplateBatchFiles/Utility/ReadDelimitedFiles.bf
  445. lib/hyphy/TemplateBatchFiles/Utility/TreeFunctions.bf
  446. lib/hyphy/TemplateBatchFiles/Utility/WriteDelimitedFiles.bf
  447. lib/hyphy/TemplateBatchFiles/WANC.bf
  448. lib/hyphy/TemplateBatchFiles/WebUpdate.bf
  449. lib/hyphy/TemplateBatchFiles/YangNielsenBranchSite2005.bf
  450. lib/hyphy/TemplateBatchFiles/_BMS_Aux.ibf
  451. lib/hyphy/TemplateBatchFiles/_CMS_Aux.ibf
  452. lib/hyphy/TemplateBatchFiles/_MFReader_.ibf
  453. lib/hyphy/TemplateBatchFiles/_MSCOneStep.ibf
  454. lib/hyphy/TemplateBatchFiles/_tipDater.ibf
  455. lib/hyphy/TemplateBatchFiles/bayesgraph.ibf
  456. lib/hyphy/TemplateBatchFiles/binomial.ibf
  457. lib/hyphy/TemplateBatchFiles/branchSwappingFunctions.bf
  458. lib/hyphy/TemplateBatchFiles/categoryEcho.bf
  459. lib/hyphy/TemplateBatchFiles/chooseDistanceFormula.def
  460. lib/hyphy/TemplateBatchFiles/dNdSBivariateRateAnalysis.bf
  461. lib/hyphy/TemplateBatchFiles/dNdSBivariateRateAnalysis_CompareDS.bf
  462. lib/hyphy/TemplateBatchFiles/dNdSDistributionComparison.bf
  463. lib/hyphy/TemplateBatchFiles/dNdSDistributionComparisonPartitions.bf
  464. lib/hyphy/TemplateBatchFiles/dNdSRateAnalysis.bf
  465. lib/hyphy/TemplateBatchFiles/dNdSRateAnalysis_MF.bf
  466. lib/hyphy/TemplateBatchFiles/dNdSResultProcessor.bf
  467. lib/hyphy/TemplateBatchFiles/dSdNTreeTools.ibf
  468. lib/hyphy/TemplateBatchFiles/distanceMethodNPBootstrap.bf
  469. lib/hyphy/TemplateBatchFiles/distanceRMethodNPBootstrap.bf
  470. lib/hyphy/TemplateBatchFiles/doNNISwap.bf
  471. lib/hyphy/TemplateBatchFiles/doSPRSwap.bf
  472. lib/hyphy/TemplateBatchFiles/files.lst
  473. lib/hyphy/TemplateBatchFiles/globalChecker.ibf
  474. lib/hyphy/TemplateBatchFiles/heuristicMethodNPBootstrap.bf
  475. lib/hyphy/TemplateBatchFiles/last.date
  476. lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf
  477. lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
  478. lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
  479. lib/hyphy/TemplateBatchFiles/libv3/convenience/math.bf
  480. lib/hyphy/TemplateBatchFiles/libv3/convenience/matrix.bf
  481. lib/hyphy/TemplateBatchFiles/libv3/convenience/random.bf
  482. lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf
  483. lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf
  484. lib/hyphy/TemplateBatchFiles/libv3/models/DNA/GTR.bf
  485. lib/hyphy/TemplateBatchFiles/libv3/models/DNA/HKY85.bf
  486. lib/hyphy/TemplateBatchFiles/libv3/models/DNA/JC69.bf
  487. lib/hyphy/TemplateBatchFiles/libv3/models/binary.bf
  488. lib/hyphy/TemplateBatchFiles/libv3/models/binary/charbinary.bf
  489. lib/hyphy/TemplateBatchFiles/libv3/models/binary/empirical.bf
  490. lib/hyphy/TemplateBatchFiles/libv3/models/codon.bf
  491. lib/hyphy/TemplateBatchFiles/libv3/models/codon/BS_REL.bf
  492. lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV.bf
  493. lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV_MH.bf
  494. lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf
  495. lib/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf
  496. lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf
  497. lib/hyphy/TemplateBatchFiles/libv3/models/protein.bf
  498. lib/hyphy/TemplateBatchFiles/libv3/models/protein/REV.bf
  499. lib/hyphy/TemplateBatchFiles/libv3/models/protein/empirical.bf
  500. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/HIV.ibf
  501. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/JC69.ibf
  502. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/JTT.ibf
  503. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/LG.ibf
  504. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/WAG.ibf
  505. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/gcpREV.ibf
  506. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/mt.ibf
  507. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrix2dict_aux.bf
  508. lib/hyphy/TemplateBatchFiles/libv3/models/rate_variation.bf
  509. lib/hyphy/TemplateBatchFiles/libv3/stats.bf
  510. lib/hyphy/TemplateBatchFiles/libv3/tasks/alignments.bf
  511. lib/hyphy/TemplateBatchFiles/libv3/tasks/ancestral.bf
  512. lib/hyphy/TemplateBatchFiles/libv3/tasks/bayesgraph.ibf
  513. lib/hyphy/TemplateBatchFiles/libv3/tasks/estimators.bf
  514. lib/hyphy/TemplateBatchFiles/libv3/tasks/genetic_code.bf
  515. lib/hyphy/TemplateBatchFiles/libv3/tasks/mpi.bf
  516. lib/hyphy/TemplateBatchFiles/libv3/tasks/trees.bf
  517. lib/hyphy/TemplateBatchFiles/molclockBootstrap.bf
  518. lib/hyphy/TemplateBatchFiles/pairwiseDistanceEstimator.ibf
  519. lib/hyphy/TemplateBatchFiles/pairwiseDistanceEstimatorCounter.ibf
  520. lib/hyphy/TemplateBatchFiles/partitionSequences.ibf
  521. lib/hyphy/TemplateBatchFiles/post_ancestors.bf
  522. lib/hyphy/TemplateBatchFiles/post_counting.bf
  523. lib/hyphy/TemplateBatchFiles/post_covariance.bf
  524. lib/hyphy/TemplateBatchFiles/post_dNdS.bf
  525. lib/hyphy/TemplateBatchFiles/post_lfprofile.bf
  526. lib/hyphy/TemplateBatchFiles/post_npbs.bf
  527. lib/hyphy/TemplateBatchFiles/post_pbs.bf
  528. lib/hyphy/TemplateBatchFiles/post_sampler.bf
  529. lib/hyphy/TemplateBatchFiles/post_saveResults.bf
  530. lib/hyphy/TemplateBatchFiles/post_sns.bf
  531. lib/hyphy/TemplateBatchFiles/post_variance.bf
  532. lib/hyphy/TemplateBatchFiles/post_viewResults.bf
  533. lib/hyphy/TemplateBatchFiles/postprocessors.lst
  534. lib/hyphy/TemplateBatchFiles/qndhelper1.ibf
  535. lib/hyphy/TemplateBatchFiles/qndhelper1_mf.ibf
  536. lib/hyphy/TemplateBatchFiles/qndhelper2.ibf
  537. lib/hyphy/TemplateBatchFiles/qndhelper2_mf.ibf
  538. lib/hyphy/TemplateBatchFiles/qndhelper3.ibf
  539. lib/hyphy/TemplateBatchFiles/qndhelper4.ibf
  540. lib/hyphy/TemplateBatchFiles/queryTree.bf
  541. lib/hyphy/TemplateBatchFiles/readIndexFile.bf
  542. lib/hyphy/TemplateBatchFiles/relrateBootstrap.bf
  543. lib/hyphy/TemplateBatchFiles/relrateBootstrapL.bf
  544. lib/hyphy/TemplateBatchFiles/relratioBootstrap.bf
  545. lib/hyphy/TemplateBatchFiles/selectModelParameters.bf
  546. lib/hyphy/TemplateBatchFiles/simpleBootstrap.bf
  547. lib/hyphy/TopologyInference/Exhaustive_Search
  548. lib/hyphy/TopologyInference/Neighbor_Joining
  549. lib/hyphy/TopologyInference/Sequential_Addition
  550. lib/hyphy/TopologyInference/Star_Decomposition
  551. lib/hyphy/TopologyInference/Support/branchSwappingFunctions.bf
  552. lib/hyphy/TopologyInference/Support/doNNISwap.bf
  553. lib/hyphy/TopologyInference/Support/doSPRSwap.bf
  554. lib/hyphy/TreeAddIns/Splits
  555. lib/hyphy/TreeAddIns/Tree Statistics
  556. lib/hyphy/UserAddins/AAContent
  557. lib/hyphy/UserAddins/BatchFileByURL
  558. lib/hyphy/UserAddins/BranchLengthCI
  559. lib/hyphy/UserAddins/CodonMutationToTreeMapper
  560. lib/hyphy/UserAddins/CountSubstitutions
  561. lib/hyphy/UserAddins/ExportLikelihoodFunction
  562. lib/hyphy/UserAddins/GenBankSequences
  563. lib/hyphy/UserAddins/Includes/ChooseALF.ibf
  564. lib/hyphy/UserAddins/Includes/MappersHelp.ibf
  565. lib/hyphy/UserAddins/Includes/MappersHelpAA.ibf
  566. lib/hyphy/UserAddins/LRT
  567. lib/hyphy/UserAddins/ListUserFunctions
  568. lib/hyphy/UserAddins/MapSubstitutions
  569. lib/hyphy/UserAddins/MeanPairwiseDivergence
  570. lib/hyphy/UserAddins/MeanPairwiseDivergenceSubset
  571. lib/hyphy/UserAddins/ModelCounter
  572. lib/hyphy/UserAddins/OldAddins/AAMutationCounter
  573. lib/hyphy/UserAddins/OldAddins/CodonMutationToTreeMapper.bf
  574. lib/hyphy/UserAddins/OldAddins/ColorPSTree
  575. lib/hyphy/UserAddins/OldAddins/ConvergentAndParallel
  576. lib/hyphy/UserAddins/OldAddins/CopyBranchLengths
  577. lib/hyphy/UserAddins/OldAddins/DashPSTree
  578. lib/hyphy/UserAddins/OldAddins/ExpsPerDirection
  579. lib/hyphy/UserAddins/OldAddins/FilterAssignments
  580. lib/hyphy/UserAddins/OldAddins/InferredAASubstitutionsCounter
  581. lib/hyphy/UserAddins/OldAddins/LocaldNdS
  582. lib/hyphy/UserAddins/OldAddins/ModelFitSummary
  583. lib/hyphy/UserAddins/OldAddins/ModelFitSummaryAA
  584. lib/hyphy/UserAddins/OldAddins/Multiclass DN DS inference
  585. lib/hyphy/UserAddins/OldAddins/PartitionBranchesByClasses
  586. lib/hyphy/UserAddins/OldAddins/PredictivePosteriorP
  587. lib/hyphy/UserAddins/OldAddins/RNARateMatrix
  588. lib/hyphy/UserAddins/OldAddins/SimulateAndTabDN_DS
  589. lib/hyphy/UserAddins/OldAddins/SimulateFromLF
  590. lib/hyphy/UserAddins/OldAddins/TreeLengthConstraint
  591. lib/hyphy/UserAddins/OldAddins/dNanddSTrees.bf
  592. lib/hyphy/UserAddins/OldAddins/dS and dN factors
  593. lib/hyphy/UserAddins/RecombinationProcessor.bf
  594. lib/hyphy/UserAddins/SimulateFromLF
  595. lib/hyphy/UserAddins/Tidbits
  596. lib/hyphy/data/brown.nuc
  597. lib/hyphy/data/integrase_BDA.nex
  598. lib/hyphy/data/p51.aa
  599. lib/hyphy/data/p51.nex
  600. Collapse this list.

To install the port: cd /usr/ports/biology/hyphy/ && make install clean
To add the package: pkg install hyphy

PKGNAME: hyphy

ONLY_FOR_ARCHS: amd64 i386

distinfo:

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


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. cmake : devel/cmake
  2. ninja : devel/ninja
Library dependencies:
  1. libcurl.so : ftp/curl
There are no ports dependent upon this port

Configuration Options
     No options to configure

USES:
compiler:c++14-lang cmake:outsource localbase:ldflags ssl

Master Sites:
  1. https://codeload.github.com/veg/hyphy/tar.gz/2.3.14-16-g3d88d3e6?dummy=/

Number of commits found: 4

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
20 Oct 2018 12:21:15
Original commit files touched by this commit  2.3.14.16
Revision:482495
jrm search for other commits by this committer
biology/hyphy: Update to version 2.3.14.16

This pulls in fixes after the 2.3.14 release.

Upstream changes for version 2.3.14:
https://github.com/veg/hyphy/releases/tag/2.3.14

Subsequent fixes:
https://github.com/veg/hyphy/commit/1ecac31
https://github.com/veg/hyphy/commit/bec6833
https://github.com/veg/hyphy/commit/9847438
https://github.com/veg/hyphy/commit/02dcedd
https://github.com/veg/hyphy/commit/8f44d3c
https://github.com/veg/hyphy/commit/5297c30
https://github.com/veg/hyphy/commit/3d88d3e
22 May 2018 22:55:18
Original commit files touched by this commit  2.3.13
Revision:470664
jrm search for other commits by this committer
biology/hyphy: Update to version 2.3.13
14 May 2018 16:52:40
Original commit files touched by this commit  2.3.12_1
Revision:469922
jrm search for other commits by this committer
biology/hyphy: Bump PORTREVISION after upstream rerolled release

Also, remove patch that upstream incorporated in new tarball.

Upstream issue: https://github.com/veg/hyphy/issues/796
11 May 2018 00:05:16
Original commit files touched by this commit  2.3.12
Revision:469604
jrm search for other commits by this committer
New port, biology/hyphy: Hypothesis testing using Phylogenies

WWW: http://www.hyphy.org/

Number of commits found: 4

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