FreshPorts -- The Place For Ports notbugIf you buy from Amazon USA, please support us by using this link.
Follow us
Blog
Twitter

test-nginx01 & pg02
Port details
hyphy Hypothesis testing using Phylogenies
2.3.13 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 (596 items)
  1. /usr/local/share/licenses/hyphy-2.3.13/catalog.mk
  2. /usr/local/share/licenses/hyphy-2.3.13/LICENSE
  3. /usr/local/share/licenses/hyphy-2.3.13/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/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/aBSREL.bf
  274. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/grid_compute.ibf
  275. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf
  276. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf
  277. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf
  278. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/testers/FitModel.bf
  279. lib/hyphy/TemplateBatchFiles/SelectionLRT.bf
  280. lib/hyphy/TemplateBatchFiles/SeqAlignShared.ibf
  281. lib/hyphy/TemplateBatchFiles/SeqAlignment.bf
  282. lib/hyphy/TemplateBatchFiles/SeqAlignmentCodon.bf
  283. lib/hyphy/TemplateBatchFiles/SeqAlignmentCodonShared.ibf
  284. lib/hyphy/TemplateBatchFiles/SeqAlignmentNuc.bf
  285. lib/hyphy/TemplateBatchFiles/SeqAlignmentNucShared.ibf
  286. lib/hyphy/TemplateBatchFiles/SeqAlignmentProt.bf
  287. lib/hyphy/TemplateBatchFiles/SeqAlignmentTop75.bf
  288. lib/hyphy/TemplateBatchFiles/SequentialAddition.bf
  289. lib/hyphy/TemplateBatchFiles/SequentialAddition.ibf
  290. lib/hyphy/TemplateBatchFiles/SimilarityPlot.bf
  291. lib/hyphy/TemplateBatchFiles/SimmondsAI.bf
  292. lib/hyphy/TemplateBatchFiles/SimpleMutationCounter.bf
  293. lib/hyphy/TemplateBatchFiles/SingleBreakpointRecomb-2.bf
  294. lib/hyphy/TemplateBatchFiles/SingleBreakpointRecomb.bf
  295. lib/hyphy/TemplateBatchFiles/SiteRates.bf
  296. lib/hyphy/TemplateBatchFiles/SiteRates2.bf
  297. lib/hyphy/TemplateBatchFiles/SlatkinMaddison-2parts.bf
  298. lib/hyphy/TemplateBatchFiles/SlatkinMaddison.bf
  299. lib/hyphy/TemplateBatchFiles/SlidingNucWindow.bf
  300. lib/hyphy/TemplateBatchFiles/SlidingWindowAnalysis.bf
  301. lib/hyphy/TemplateBatchFiles/SplitSequencesByPattern.bf
  302. lib/hyphy/TemplateBatchFiles/StarDecomposition.bf
  303. lib/hyphy/TemplateBatchFiles/StrandGRMTest.bf
  304. lib/hyphy/TemplateBatchFiles/StripStopCodons.bf
  305. lib/hyphy/TemplateBatchFiles/SubtreeSelectionComparison.bf
  306. lib/hyphy/TemplateBatchFiles/TemplateModels/190
  307. lib/hyphy/TemplateBatchFiles/TemplateModels/BranchSiteTemplate.mdl
  308. lib/hyphy/TemplateBatchFiles/TemplateModels/CF3x4.bf
  309. lib/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA.mdl
  310. lib/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA_empirical.mdl
  311. lib/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff.mdl
  312. lib/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff_F.mdl
  313. lib/hyphy/TemplateBatchFiles/TemplateModels/Default
  314. lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F+omega.mdl
  315. lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F.mdl
  316. lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F3x4.mdl
  317. lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+MLFREQS.mdl
  318. lib/hyphy/TemplateBatchFiles/TemplateModels/ECM.mdl
  319. lib/hyphy/TemplateBatchFiles/TemplateModels/EIAA.mdl
  320. lib/hyphy/TemplateBatchFiles/TemplateModels/EIAAFreq.mdl
  321. lib/hyphy/TemplateBatchFiles/TemplateModels/EX.dat
  322. lib/hyphy/TemplateBatchFiles/TemplateModels/EX.mdl
  323. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/BLOSUM62
  324. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/Dayhoff
  325. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/H5N1
  326. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVBetween
  327. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVWithin
  328. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/IAV
  329. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/JTT
  330. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LCAP
  331. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LG
  332. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/MtArt
  333. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/VT
  334. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/WAG
  335. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/cpREV
  336. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/modellist.ibf
  337. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtMAM
  338. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtREV24
  339. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/rtREV
  340. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECM
  341. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECMu
  342. lib/hyphy/TemplateBatchFiles/TemplateModels/F81.mdl
  343. lib/hyphy/TemplateBatchFiles/TemplateModels/F81_binary.mdl
  344. lib/hyphy/TemplateBatchFiles/TemplateModels/F84.mdl
  345. lib/hyphy/TemplateBatchFiles/TemplateModels/F84P.mdl
  346. lib/hyphy/TemplateBatchFiles/TemplateModels/GRM.mdl
  347. lib/hyphy/TemplateBatchFiles/TemplateModels/GY94.ibf
  348. lib/hyphy/TemplateBatchFiles/TemplateModels/GY94.mdl
  349. lib/hyphy/TemplateBatchFiles/TemplateModels/GY94customF3x4.mdl
  350. lib/hyphy/TemplateBatchFiles/TemplateModels/GY94w9.mdl
  351. lib/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween+F.mdl
  352. lib/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.ibf
  353. lib/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.mdl
  354. lib/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin+F.mdl
  355. lib/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.ibf
  356. lib/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.mdl
  357. lib/hyphy/TemplateBatchFiles/TemplateModels/HKY85.mdl
  358. lib/hyphy/TemplateBatchFiles/TemplateModels/JC69.mdl
  359. lib/hyphy/TemplateBatchFiles/TemplateModels/JC69_binary.mdl
  360. lib/hyphy/TemplateBatchFiles/TemplateModels/Jones.mdl
  361. lib/hyphy/TemplateBatchFiles/TemplateModels/Jones_F.mdl
  362. lib/hyphy/TemplateBatchFiles/TemplateModels/K2P.mdl
  363. lib/hyphy/TemplateBatchFiles/TemplateModels/K3ST.mdl
  364. lib/hyphy/TemplateBatchFiles/TemplateModels/LCAP.mdl
  365. lib/hyphy/TemplateBatchFiles/TemplateModels/MEC.mdl
  366. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94.mdl
  367. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94custom.mdl
  368. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94customCF3x4.mdl
  369. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94customF1x4.mdl
  370. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94customFreqs.mdl
  371. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAA.mdl
  372. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAF61.mdl
  373. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAF61multiple.mdl
  374. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAFreqs.mdl
  375. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAUserFreqs.mdl
  376. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wEX.mdl
  377. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94with9freqs.mdl
  378. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94x2.mdl
  379. lib/hyphy/TemplateBatchFiles/TemplateModels/MGFreqsEstimator.ibf
  380. lib/hyphy/TemplateBatchFiles/TemplateModels/MGwAA.ibf
  381. lib/hyphy/TemplateBatchFiles/TemplateModels/MGwEX.ibf
  382. lib/hyphy/TemplateBatchFiles/TemplateModels/NRM+Freqs.mdl
  383. lib/hyphy/TemplateBatchFiles/TemplateModels/NRM.mdl
  384. lib/hyphy/TemplateBatchFiles/TemplateModels/PCH
  385. lib/hyphy/TemplateBatchFiles/TemplateModels/RNA16.mdl
  386. lib/hyphy/TemplateBatchFiles/TemplateModels/RNA16A
  387. lib/hyphy/TemplateBatchFiles/TemplateModels/RNA16SvH.mdl
  388. lib/hyphy/TemplateBatchFiles/TemplateModels/RNAEqualInput
  389. lib/hyphy/TemplateBatchFiles/TemplateModels/RNAF81
  390. lib/hyphy/TemplateBatchFiles/TemplateModels/RNAMuse95.mdl
  391. lib/hyphy/TemplateBatchFiles/TemplateModels/RNAREV
  392. lib/hyphy/TemplateBatchFiles/TemplateModels/RNAREV_1
  393. lib/hyphy/TemplateBatchFiles/TemplateModels/S4
  394. lib/hyphy/TemplateBatchFiles/TemplateModels/STGRM.mdl
  395. lib/hyphy/TemplateBatchFiles/TemplateModels/TrN.mdl
  396. lib/hyphy/TemplateBatchFiles/TemplateModels/UniversalCode.def
  397. lib/hyphy/TemplateBatchFiles/TemplateModels/WAG.mdl
  398. lib/hyphy/TemplateBatchFiles/TemplateModels/WAG_F.mdl
  399. lib/hyphy/TemplateBatchFiles/TemplateModels/Yang2000Distributions.def
  400. lib/hyphy/TemplateBatchFiles/TemplateModels/chooseGeneticCode.def
  401. lib/hyphy/TemplateBatchFiles/TemplateModels/custm4x4.mdl
  402. lib/hyphy/TemplateBatchFiles/TemplateModels/defineGamma.mdl
  403. lib/hyphy/TemplateBatchFiles/TemplateModels/defineHM.mdl
  404. lib/hyphy/TemplateBatchFiles/TemplateModels/fitness.mdl
  405. lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters.mdl
  406. lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters2.mdl
  407. lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters3.mdl
  408. lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters4.mdl
  409. lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters5.mdl
  410. lib/hyphy/TemplateBatchFiles/TemplateModels/models.lst
  411. lib/hyphy/TemplateBatchFiles/TemplateModels/mtMAM.mdl
  412. lib/hyphy/TemplateBatchFiles/TemplateModels/mtMAM_F.mdl
  413. lib/hyphy/TemplateBatchFiles/TemplateModels/mtREV.mdl
  414. lib/hyphy/TemplateBatchFiles/TemplateModels/mtREV_24.mdl
  415. lib/hyphy/TemplateBatchFiles/TemplateModels/mtREV_24_F.mdl
  416. lib/hyphy/TemplateBatchFiles/TemplateModels/reducedREV.mdl
  417. lib/hyphy/TemplateBatchFiles/TemplateModels/rtREV.mdl
  418. lib/hyphy/TemplateBatchFiles/TemplateModels/rtREV_F.mdl
  419. lib/hyphy/TemplateBatchFiles/TestBranchDNDS.bf
  420. lib/hyphy/TemplateBatchFiles/TestClade.bf
  421. lib/hyphy/TemplateBatchFiles/TestCladeMeans.bf
  422. lib/hyphy/TemplateBatchFiles/TopologySearch.bf
  423. lib/hyphy/TemplateBatchFiles/TopologySearchConstrained.bf
  424. lib/hyphy/TemplateBatchFiles/TreeCorrelationCoefficients.bf
  425. lib/hyphy/TemplateBatchFiles/TreeTools.ibf
  426. lib/hyphy/TemplateBatchFiles/UpperBound.bf
  427. lib/hyphy/TemplateBatchFiles/Utility/AncestralMapper.bf
  428. lib/hyphy/TemplateBatchFiles/Utility/BranchLengthFitters.bf
  429. lib/hyphy/TemplateBatchFiles/Utility/CoalescentPostProcessor.bf
  430. lib/hyphy/TemplateBatchFiles/Utility/CodonTools.bf
  431. lib/hyphy/TemplateBatchFiles/Utility/DBTools.ibf
  432. lib/hyphy/TemplateBatchFiles/Utility/DescriptiveStatistics.bf
  433. lib/hyphy/TemplateBatchFiles/Utility/GrabBag.bf
  434. lib/hyphy/TemplateBatchFiles/Utility/HXB2Mapper.bf
  435. lib/hyphy/TemplateBatchFiles/Utility/LocalMGREV.bf
  436. lib/hyphy/TemplateBatchFiles/Utility/LocalMGREVMLFreqs.bf
  437. lib/hyphy/TemplateBatchFiles/Utility/MPITools.bf
  438. lib/hyphy/TemplateBatchFiles/Utility/NJ.bf
  439. lib/hyphy/TemplateBatchFiles/Utility/PS_Plotters.bf
  440. lib/hyphy/TemplateBatchFiles/Utility/PostScript.bf
  441. lib/hyphy/TemplateBatchFiles/Utility/ProbabilityDistributions.bf
  442. lib/hyphy/TemplateBatchFiles/Utility/ReadDelimitedFiles.bf
  443. lib/hyphy/TemplateBatchFiles/Utility/TreeFunctions.bf
  444. lib/hyphy/TemplateBatchFiles/Utility/WriteDelimitedFiles.bf
  445. lib/hyphy/TemplateBatchFiles/WANC.bf
  446. lib/hyphy/TemplateBatchFiles/WebUpdate.bf
  447. lib/hyphy/TemplateBatchFiles/YangNielsenBranchSite2005.bf
  448. lib/hyphy/TemplateBatchFiles/_BMS_Aux.ibf
  449. lib/hyphy/TemplateBatchFiles/_CMS_Aux.ibf
  450. lib/hyphy/TemplateBatchFiles/_MFReader_.ibf
  451. lib/hyphy/TemplateBatchFiles/_MSCOneStep.ibf
  452. lib/hyphy/TemplateBatchFiles/_tipDater.ibf
  453. lib/hyphy/TemplateBatchFiles/bayesgraph.ibf
  454. lib/hyphy/TemplateBatchFiles/binomial.ibf
  455. lib/hyphy/TemplateBatchFiles/branchSwappingFunctions.bf
  456. lib/hyphy/TemplateBatchFiles/categoryEcho.bf
  457. lib/hyphy/TemplateBatchFiles/chooseDistanceFormula.def
  458. lib/hyphy/TemplateBatchFiles/dNdSBivariateRateAnalysis.bf
  459. lib/hyphy/TemplateBatchFiles/dNdSBivariateRateAnalysis_CompareDS.bf
  460. lib/hyphy/TemplateBatchFiles/dNdSDistributionComparison.bf
  461. lib/hyphy/TemplateBatchFiles/dNdSDistributionComparisonPartitions.bf
  462. lib/hyphy/TemplateBatchFiles/dNdSRateAnalysis.bf
  463. lib/hyphy/TemplateBatchFiles/dNdSRateAnalysis_MF.bf
  464. lib/hyphy/TemplateBatchFiles/dNdSResultProcessor.bf
  465. lib/hyphy/TemplateBatchFiles/dSdNTreeTools.ibf
  466. lib/hyphy/TemplateBatchFiles/distanceMethodNPBootstrap.bf
  467. lib/hyphy/TemplateBatchFiles/distanceRMethodNPBootstrap.bf
  468. lib/hyphy/TemplateBatchFiles/doNNISwap.bf
  469. lib/hyphy/TemplateBatchFiles/doSPRSwap.bf
  470. lib/hyphy/TemplateBatchFiles/files.lst
  471. lib/hyphy/TemplateBatchFiles/globalChecker.ibf
  472. lib/hyphy/TemplateBatchFiles/heuristicMethodNPBootstrap.bf
  473. lib/hyphy/TemplateBatchFiles/last.date
  474. lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf
  475. lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
  476. lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
  477. lib/hyphy/TemplateBatchFiles/libv3/convenience/math.bf
  478. lib/hyphy/TemplateBatchFiles/libv3/convenience/matrix.bf
  479. lib/hyphy/TemplateBatchFiles/libv3/convenience/random.bf
  480. lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf
  481. lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf
  482. lib/hyphy/TemplateBatchFiles/libv3/models/DNA/GTR.bf
  483. lib/hyphy/TemplateBatchFiles/libv3/models/DNA/HKY85.bf
  484. lib/hyphy/TemplateBatchFiles/libv3/models/DNA/JC69.bf
  485. lib/hyphy/TemplateBatchFiles/libv3/models/binary.bf
  486. lib/hyphy/TemplateBatchFiles/libv3/models/binary/charbinary.bf
  487. lib/hyphy/TemplateBatchFiles/libv3/models/binary/empirical.bf
  488. lib/hyphy/TemplateBatchFiles/libv3/models/codon.bf
  489. lib/hyphy/TemplateBatchFiles/libv3/models/codon/BS_REL.bf
  490. lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV.bf
  491. lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV_MH.bf
  492. lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf
  493. lib/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf
  494. lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf
  495. lib/hyphy/TemplateBatchFiles/libv3/models/protein.bf
  496. lib/hyphy/TemplateBatchFiles/libv3/models/protein/REV.bf
  497. lib/hyphy/TemplateBatchFiles/libv3/models/protein/empirical.bf
  498. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/HIV.ibf
  499. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/JC69.ibf
  500. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/JTT.ibf
  501. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/LG.ibf
  502. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/WAG.ibf
  503. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/gcpREV.ibf
  504. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/mt.ibf
  505. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrix2dict_aux.bf
  506. lib/hyphy/TemplateBatchFiles/libv3/models/rate_variation.bf
  507. lib/hyphy/TemplateBatchFiles/libv3/stats.bf
  508. lib/hyphy/TemplateBatchFiles/libv3/tasks/alignments.bf
  509. lib/hyphy/TemplateBatchFiles/libv3/tasks/ancestral.bf
  510. lib/hyphy/TemplateBatchFiles/libv3/tasks/estimators.bf
  511. lib/hyphy/TemplateBatchFiles/libv3/tasks/genetic_code.bf
  512. lib/hyphy/TemplateBatchFiles/libv3/tasks/mpi.bf
  513. lib/hyphy/TemplateBatchFiles/libv3/tasks/trees.bf
  514. lib/hyphy/TemplateBatchFiles/molclockBootstrap.bf
  515. lib/hyphy/TemplateBatchFiles/pairwiseDistanceEstimator.ibf
  516. lib/hyphy/TemplateBatchFiles/pairwiseDistanceEstimatorCounter.ibf
  517. lib/hyphy/TemplateBatchFiles/partitionSequences.ibf
  518. lib/hyphy/TemplateBatchFiles/post_ancestors.bf
  519. lib/hyphy/TemplateBatchFiles/post_counting.bf
  520. lib/hyphy/TemplateBatchFiles/post_covariance.bf
  521. lib/hyphy/TemplateBatchFiles/post_dNdS.bf
  522. lib/hyphy/TemplateBatchFiles/post_lfprofile.bf
  523. lib/hyphy/TemplateBatchFiles/post_npbs.bf
  524. lib/hyphy/TemplateBatchFiles/post_pbs.bf
  525. lib/hyphy/TemplateBatchFiles/post_sampler.bf
  526. lib/hyphy/TemplateBatchFiles/post_saveResults.bf
  527. lib/hyphy/TemplateBatchFiles/post_sns.bf
  528. lib/hyphy/TemplateBatchFiles/post_variance.bf
  529. lib/hyphy/TemplateBatchFiles/post_viewResults.bf
  530. lib/hyphy/TemplateBatchFiles/postprocessors.lst
  531. lib/hyphy/TemplateBatchFiles/qndhelper1.ibf
  532. lib/hyphy/TemplateBatchFiles/qndhelper1_mf.ibf
  533. lib/hyphy/TemplateBatchFiles/qndhelper2.ibf
  534. lib/hyphy/TemplateBatchFiles/qndhelper2_mf.ibf
  535. lib/hyphy/TemplateBatchFiles/qndhelper3.ibf
  536. lib/hyphy/TemplateBatchFiles/qndhelper4.ibf
  537. lib/hyphy/TemplateBatchFiles/queryTree.bf
  538. lib/hyphy/TemplateBatchFiles/readIndexFile.bf
  539. lib/hyphy/TemplateBatchFiles/relrateBootstrap.bf
  540. lib/hyphy/TemplateBatchFiles/relrateBootstrapL.bf
  541. lib/hyphy/TemplateBatchFiles/relratioBootstrap.bf
  542. lib/hyphy/TemplateBatchFiles/selectModelParameters.bf
  543. lib/hyphy/TemplateBatchFiles/simpleBootstrap.bf
  544. lib/hyphy/TopologyInference/Exhaustive_Search
  545. lib/hyphy/TopologyInference/Neighbor_Joining
  546. lib/hyphy/TopologyInference/Sequential_Addition
  547. lib/hyphy/TopologyInference/Star_Decomposition
  548. lib/hyphy/TopologyInference/Support/branchSwappingFunctions.bf
  549. lib/hyphy/TopologyInference/Support/doNNISwap.bf
  550. lib/hyphy/TopologyInference/Support/doSPRSwap.bf
  551. lib/hyphy/TreeAddIns/Splits
  552. lib/hyphy/TreeAddIns/Tree Statistics
  553. lib/hyphy/UserAddins/AAContent
  554. lib/hyphy/UserAddins/BatchFileByURL
  555. lib/hyphy/UserAddins/BranchLengthCI
  556. lib/hyphy/UserAddins/CodonMutationToTreeMapper
  557. lib/hyphy/UserAddins/CountSubstitutions
  558. lib/hyphy/UserAddins/ExportLikelihoodFunction
  559. lib/hyphy/UserAddins/GenBankSequences
  560. lib/hyphy/UserAddins/Includes/ChooseALF.ibf
  561. lib/hyphy/UserAddins/Includes/MappersHelp.ibf
  562. lib/hyphy/UserAddins/Includes/MappersHelpAA.ibf
  563. lib/hyphy/UserAddins/LRT
  564. lib/hyphy/UserAddins/ListUserFunctions
  565. lib/hyphy/UserAddins/MapSubstitutions
  566. lib/hyphy/UserAddins/MeanPairwiseDivergence
  567. lib/hyphy/UserAddins/MeanPairwiseDivergenceSubset
  568. lib/hyphy/UserAddins/ModelCounter
  569. lib/hyphy/UserAddins/OldAddins/AAMutationCounter
  570. lib/hyphy/UserAddins/OldAddins/CodonMutationToTreeMapper.bf
  571. lib/hyphy/UserAddins/OldAddins/ColorPSTree
  572. lib/hyphy/UserAddins/OldAddins/ConvergentAndParallel
  573. lib/hyphy/UserAddins/OldAddins/CopyBranchLengths
  574. lib/hyphy/UserAddins/OldAddins/DashPSTree
  575. lib/hyphy/UserAddins/OldAddins/ExpsPerDirection
  576. lib/hyphy/UserAddins/OldAddins/FilterAssignments
  577. lib/hyphy/UserAddins/OldAddins/InferredAASubstitutionsCounter
  578. lib/hyphy/UserAddins/OldAddins/LocaldNdS
  579. lib/hyphy/UserAddins/OldAddins/ModelFitSummary
  580. lib/hyphy/UserAddins/OldAddins/ModelFitSummaryAA
  581. lib/hyphy/UserAddins/OldAddins/Multiclass DN DS inference
  582. lib/hyphy/UserAddins/OldAddins/PartitionBranchesByClasses
  583. lib/hyphy/UserAddins/OldAddins/PredictivePosteriorP
  584. lib/hyphy/UserAddins/OldAddins/RNARateMatrix
  585. lib/hyphy/UserAddins/OldAddins/SimulateAndTabDN_DS
  586. lib/hyphy/UserAddins/OldAddins/SimulateFromLF
  587. lib/hyphy/UserAddins/OldAddins/TreeLengthConstraint
  588. lib/hyphy/UserAddins/OldAddins/dNanddSTrees.bf
  589. lib/hyphy/UserAddins/OldAddins/dS and dN factors
  590. lib/hyphy/UserAddins/RecombinationProcessor.bf
  591. lib/hyphy/UserAddins/SimulateFromLF
  592. lib/hyphy/UserAddins/Tidbits
  593. lib/hyphy/data/brown.nuc
  594. lib/hyphy/data/integrase_BDA.nex
  595. lib/hyphy/data/p51.aa
  596. lib/hyphy/data/p51.nex
  597. 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 = 1527024059
SHA256 (veg-hyphy-2.3.13_GH0.tar.gz) = 29b72574302c98d38a92d5316b9283caa80a54c3e74c5e278c5bc9ae3d3df499
SIZE (veg-hyphy-2.3.13_GH0.tar.gz) = 7910770


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/2.3.13?dummy=/

Number of commits found: 3

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
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: 3

Login
User Login
Create account

Servers and bandwidth provided by
New York Internet, SuperNews, and RootBSD

This site
What is FreshPorts?
About the authors
Issues
FAQ
How big is it?
The latest upgrade!
Privacy
Forums
Blog
Contact

Search
Enter Keywords:
 
more...

Ports
Home
Categories
Deleted ports
Sanity Test Failures
Newsfeeds

Statistics
Graphs
NEW Graphs (Javascript)
Traffic

Servers and bandwidth provided by
New York Internet, SuperNews, and RootBSD
Valid HTML, CSS, and RSS.
Copyright © 2000-2018 Dan Langille. All rights reserved.