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Port details
hyphy Hypothesis testing using Phylogenies
2.5.8 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 2.5.8Version of this port present on the latest quarterly branch.
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-05-11 00:05:33
Last Update: 2020-03-28 12:27:11
SVN Revision: 529331
License: MIT
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (438 items)
  1. /usr/local/share/licenses/hyphy-2.5.8/catalog.mk
  2. /usr/local/share/licenses/hyphy-2.5.8/LICENSE
  3. /usr/local/share/licenses/hyphy-2.5.8/MIT
  4. bin/hyphy
  5. lib/hyphy/GeneticCodes/Alt_Yeast_Nuclear.cod
  6. lib/hyphy/GeneticCodes/Ascidian_mtDNA.cod
  7. lib/hyphy/GeneticCodes/Blepharisma_Nuclear.cod
  8. lib/hyphy/GeneticCodes/Ciliate.cod
  9. lib/hyphy/GeneticCodes/Echinoderm_mtDNA.cod
  10. lib/hyphy/GeneticCodes/Euplotid_Nuclear.cod
  11. lib/hyphy/GeneticCodes/Flatworm_mtDNA.cod
  12. lib/hyphy/GeneticCodes/Invertebrate_mtDNA.cod
  13. lib/hyphy/GeneticCodes/Mold_mtDNA.cod
  14. lib/hyphy/GeneticCodes/Thraustochytrium_mtDNA.cod
  15. lib/hyphy/GeneticCodes/Vertebratemtdna.cod
  16. lib/hyphy/GeneticCodes/Yeast_mtDNA.cod
  17. lib/hyphy/SubstitutionClasses/AAEFV/Equal
  18. lib/hyphy/SubstitutionClasses/AAEFV/Estimated
  19. lib/hyphy/SubstitutionClasses/AAEFV/Observed In Data Set
  20. lib/hyphy/SubstitutionClasses/AAEFV/Observed In Partition
  21. lib/hyphy/SubstitutionClasses/CodonEFV/Equal
  22. lib/hyphy/SubstitutionClasses/CodonEFV/Observed Codon
  23. lib/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 3 params.
  24. lib/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 9 params.
  25. lib/hyphy/SubstitutionClasses/Heterogeneity/2 Bin Discrete
  26. lib/hyphy/SubstitutionClasses/Heterogeneity/Beta
  27. lib/hyphy/SubstitutionClasses/Heterogeneity/Beta-Gamma
  28. lib/hyphy/SubstitutionClasses/Heterogeneity/General Discrete
  29. lib/hyphy/SubstitutionClasses/Heterogeneity/Half Normal
  30. lib/hyphy/SubstitutionClasses/Heterogeneity/Lognormal
  31. lib/hyphy/SubstitutionClasses/NucEFV/Equal
  32. lib/hyphy/SubstitutionClasses/NucEFV/Estimated
  33. lib/hyphy/SubstitutionClasses/NucEFV/Observed In Data Set
  34. lib/hyphy/SubstitutionClasses/NucEFV/Observed In Partition
  35. lib/hyphy/SubstitutionClasses/aa.bf
  36. lib/hyphy/SubstitutionClasses/codon.bf
  37. lib/hyphy/SubstitutionClasses/dinuc.bf
  38. lib/hyphy/SubstitutionClasses/nuc.bf
  39. lib/hyphy/SubstitutionModels/Aminoacid/Dayhoff.mdl
  40. lib/hyphy/SubstitutionModels/Aminoacid/EIAA.mdl
  41. lib/hyphy/SubstitutionModels/Aminoacid/Fitness.mdl
  42. lib/hyphy/SubstitutionModels/Aminoacid/Jones.mdl
  43. lib/hyphy/SubstitutionModels/Aminoacid/mtREV.mdl
  44. lib/hyphy/SubstitutionModels/Binary/F81.mdl
  45. lib/hyphy/SubstitutionModels/Codon/GY94_3x4.mdl
  46. lib/hyphy/SubstitutionModels/Codon/Lineage_MG94xHKY85.mdl
  47. lib/hyphy/SubstitutionModels/Codon/MG94.mdl
  48. lib/hyphy/SubstitutionModels/Codon/MG94REVOmegaCF3x4.mdl
  49. lib/hyphy/SubstitutionModels/Codon/MG94_3x4.mdl
  50. lib/hyphy/SubstitutionModels/Codon/MG94_HKY85x3_4.mdl
  51. lib/hyphy/SubstitutionModels/Codon/MG94_REV_3x4.mdl
  52. lib/hyphy/SubstitutionModels/Codon/MG94xHKY85_3x4_2Rates.mdl
  53. lib/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV.mdl
  54. lib/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV_GDD.mdl
  55. lib/hyphy/SubstitutionModels/Codon/MG94xTN93_3x4.mdl
  56. lib/hyphy/SubstitutionModels/Nucleotide/EFVEstimated.ibf
  57. lib/hyphy/SubstitutionModels/Nucleotide/F81.mdl
  58. lib/hyphy/SubstitutionModels/Nucleotide/HKY85.mdl
  59. lib/hyphy/SubstitutionModels/Nucleotide/REV.mdl
  60. lib/hyphy/SubstitutionModels/Nucleotide/REVBetaGamma.mdl
  61. lib/hyphy/SubstitutionModels/Nucleotide/TrN.mdl
  62. lib/hyphy/SubstitutionModels/User/Nucleotide/JC69
  63. lib/hyphy/SubstitutionModels/User/Nucleotide/K2P
  64. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/GY94.mdl
  65. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94GY94xREV_PARRIS_syn3.mdl
  66. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREV.mdl
  67. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate.mdl
  68. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate_Multirate.mdl
  69. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M1.def
  70. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M2.def
  71. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M3.def
  72. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_syn3.def
  73. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_synvar.def
  74. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGenerator.bf
  75. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGeneratorNoPS.bf
  76. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma1.def
  77. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2+Inv.def
  78. lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2.def
  79. lib/hyphy/TemplateBatchFiles/AAModelComparison.bf
  80. lib/hyphy/TemplateBatchFiles/AddABias.ibf
  81. lib/hyphy/TemplateBatchFiles/AnalyzeCodonData.bf
  82. lib/hyphy/TemplateBatchFiles/AnalyzeDiNucData.bf
  83. lib/hyphy/TemplateBatchFiles/AnalyzeNucDataFreq.bf
  84. lib/hyphy/TemplateBatchFiles/AnalyzeNucProtData.bf
  85. lib/hyphy/TemplateBatchFiles/BGM.bf
  86. lib/hyphy/TemplateBatchFiles/BivariateCodonRateAnalysis.bf
  87. lib/hyphy/TemplateBatchFiles/BranchSiteREL.bf
  88. lib/hyphy/TemplateBatchFiles/BranchSiteRELMultiModel.bf
  89. lib/hyphy/TemplateBatchFiles/CleanGaps.bf
  90. lib/hyphy/TemplateBatchFiles/CleanStopCodons.bf
  91. lib/hyphy/TemplateBatchFiles/ClusterAnalysis.bf
  92. lib/hyphy/TemplateBatchFiles/ClusterByDistanceRange.bf
  93. lib/hyphy/TemplateBatchFiles/CodonBivariateRateProcessor.bf
  94. lib/hyphy/TemplateBatchFiles/CodonModelCompare.bf
  95. lib/hyphy/TemplateBatchFiles/CodonToProtein.bf
  96. lib/hyphy/TemplateBatchFiles/ConvertDataFile.bf
  97. lib/hyphy/TemplateBatchFiles/DistanceMatrix.bf
  98. lib/hyphy/TemplateBatchFiles/Distances/CodonTools.def
  99. lib/hyphy/TemplateBatchFiles/Distances/CodonTools2.def
  100. lib/hyphy/TemplateBatchFiles/Distances/CodonToolsMain.def
  101. lib/hyphy/TemplateBatchFiles/Distances/JC69
  102. lib/hyphy/TemplateBatchFiles/Distances/K2P
  103. lib/hyphy/TemplateBatchFiles/Distances/K2P_RV
  104. lib/hyphy/TemplateBatchFiles/Distances/Modified_Nei_Gojobori
  105. lib/hyphy/TemplateBatchFiles/Distances/Nei_Gojobori
  106. lib/hyphy/TemplateBatchFiles/Distances/PC
  107. lib/hyphy/TemplateBatchFiles/Distances/PC_MH
  108. lib/hyphy/TemplateBatchFiles/Distances/PC_RV
  109. lib/hyphy/TemplateBatchFiles/Distances/T3P
  110. lib/hyphy/TemplateBatchFiles/Distances/TN84
  111. lib/hyphy/TemplateBatchFiles/Distances/TN93
  112. lib/hyphy/TemplateBatchFiles/Distances/TN93_RV
  113. lib/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ
  114. lib/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ_FR
  115. lib/hyphy/TemplateBatchFiles/Distances/p_Distance
  116. lib/hyphy/TemplateBatchFiles/Distances/p_Distance_aa
  117. lib/hyphy/TemplateBatchFiles/Distances/p_Distance_binary
  118. lib/hyphy/TemplateBatchFiles/Distances/p_Distance_codon
  119. lib/hyphy/TemplateBatchFiles/F_ST.bf
  120. lib/hyphy/TemplateBatchFiles/FitnessAAModels.bf
  121. lib/hyphy/TemplateBatchFiles/GARD.bf
  122. lib/hyphy/TemplateBatchFiles/GA_CHC.ibf
  123. lib/hyphy/TemplateBatchFiles/GA_CHC_Binary.ibf
  124. lib/hyphy/TemplateBatchFiles/GUI/crayolaColors.def
  125. lib/hyphy/TemplateBatchFiles/Gateaux.bf
  126. lib/hyphy/TemplateBatchFiles/GateauxMR.bf
  127. lib/hyphy/TemplateBatchFiles/KHTest.bf
  128. lib/hyphy/TemplateBatchFiles/LEISR.bf
  129. lib/hyphy/TemplateBatchFiles/LHT.bf
  130. lib/hyphy/TemplateBatchFiles/LRTRecombTest.bf
  131. lib/hyphy/TemplateBatchFiles/LZ_Complexity.bf
  132. lib/hyphy/TemplateBatchFiles/LocalMolClock.bf
  133. lib/hyphy/TemplateBatchFiles/MGvsGY.bf
  134. lib/hyphy/TemplateBatchFiles/MergeSequences.bf
  135. lib/hyphy/TemplateBatchFiles/MergeSites.bf
  136. lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/BranchAPriori.bf
  137. lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/CountSubstitutions.bf
  138. lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/EffectOfTopology.bf
  139. lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/ErrorEstimates.bf
  140. lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/LRT.bf
  141. lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/LocalvsGlobal.bf
  142. lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/NeutralExpectation.bf
  143. lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/NucleotideBiases.bf
  144. lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/Phylohandbook.bf
  145. lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/WhatsInTheMean.bf
  146. lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/dSdN.bf
  147. lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/Drosophilia_adh.nex
  148. lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/H5N1_HA_5.nex
  149. lib/hyphy/TemplateBatchFiles/ModelTest.bf
  150. lib/hyphy/TemplateBatchFiles/MolClockAllRoots.bf
  151. lib/hyphy/TemplateBatchFiles/MolecularClock.bf
  152. lib/hyphy/TemplateBatchFiles/NeighborJoining.bf
  153. lib/hyphy/TemplateBatchFiles/NielsenYang.bf
  154. lib/hyphy/TemplateBatchFiles/NucModelCompare.bf
  155. lib/hyphy/TemplateBatchFiles/PARRIS.bf
  156. lib/hyphy/TemplateBatchFiles/PairwiseRelativeRate.bf
  157. lib/hyphy/TemplateBatchFiles/PairwiseRelativeRatio.bf
  158. lib/hyphy/TemplateBatchFiles/PartitionDataFile.bf
  159. lib/hyphy/TemplateBatchFiles/ProteinAnalyses/ProteinGTRFit.bf
  160. lib/hyphy/TemplateBatchFiles/ProteinAnalyses/ProteinGTRFit_helper.ibf
  161. lib/hyphy/TemplateBatchFiles/ProteinAnalyses/README_relative_prot_rates.md
  162. lib/hyphy/TemplateBatchFiles/ProteinAnalyses/plusF_helper.ibf
  163. lib/hyphy/TemplateBatchFiles/ProteinAnalyses/relative_prot_rates.bf
  164. lib/hyphy/TemplateBatchFiles/ReduceDataSetMatrix.bf
  165. lib/hyphy/TemplateBatchFiles/RelativeRate.bf
  166. lib/hyphy/TemplateBatchFiles/RelativeRatio.bf
  167. lib/hyphy/TemplateBatchFiles/SGASimProcessor.bf
  168. lib/hyphy/TemplateBatchFiles/SGEmulator.bf
  169. lib/hyphy/TemplateBatchFiles/SGEmulator_MF.bf
  170. lib/hyphy/TemplateBatchFiles/SGIvL.bf
  171. lib/hyphy/TemplateBatchFiles/SM-2019.bf
  172. lib/hyphy/TemplateBatchFiles/Samplers/lhc-ErrorEst.bf
  173. lib/hyphy/TemplateBatchFiles/Samplers/lhc.bf
  174. lib/hyphy/TemplateBatchFiles/Samplers/lhc_supp.ibf
  175. lib/hyphy/TemplateBatchFiles/Samplers/sir.bf
  176. lib/hyphy/TemplateBatchFiles/Samplers/srs-ErrorEst.ibf
  177. lib/hyphy/TemplateBatchFiles/Samplers/srs.ibf
  178. lib/hyphy/TemplateBatchFiles/SandNSAmbigs.bf
  179. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf
  180. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/BranchSiteREL.bf
  181. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FADE.bf
  182. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FEL-contrast.bf
  183. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FEL.bf
  184. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf
  185. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/MEME.bf
  186. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/PRIME.bf
  187. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX-Groups.bf
  188. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX-SRV.bf
  189. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX.bf
  190. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/SLAC.bf
  191. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/SingleOmega.bf
  192. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf
  193. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/grid_compute.ibf
  194. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf
  195. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf
  196. lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf
  197. lib/hyphy/TemplateBatchFiles/SelectionLRT.bf
  198. lib/hyphy/TemplateBatchFiles/SeqAlignShared.ibf
  199. lib/hyphy/TemplateBatchFiles/SeqAlignmentCodon.bf
  200. lib/hyphy/TemplateBatchFiles/SeqAlignmentCodonShared.ibf
  201. lib/hyphy/TemplateBatchFiles/SeqAlignmentNucShared.ibf
  202. lib/hyphy/TemplateBatchFiles/SequentialAddition.bf
  203. lib/hyphy/TemplateBatchFiles/SequentialAddition.ibf
  204. lib/hyphy/TemplateBatchFiles/SimilarityPlot.bf
  205. lib/hyphy/TemplateBatchFiles/SimmondsAI.bf
  206. lib/hyphy/TemplateBatchFiles/SingleBreakpointRecomb.bf
  207. lib/hyphy/TemplateBatchFiles/SlidingWindowAnalysis.bf
  208. lib/hyphy/TemplateBatchFiles/TemplateModels/190
  209. lib/hyphy/TemplateBatchFiles/TemplateModels/BranchSiteTemplate.mdl
  210. lib/hyphy/TemplateBatchFiles/TemplateModels/CF3x4.bf
  211. lib/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA.mdl
  212. lib/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA_empirical.mdl
  213. lib/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff.mdl
  214. lib/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff_F.mdl
  215. lib/hyphy/TemplateBatchFiles/TemplateModels/Default
  216. lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F+omega.mdl
  217. lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F.mdl
  218. lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F3x4.mdl
  219. lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+MLFREQS.mdl
  220. lib/hyphy/TemplateBatchFiles/TemplateModels/ECM.mdl
  221. lib/hyphy/TemplateBatchFiles/TemplateModels/EIAA.mdl
  222. lib/hyphy/TemplateBatchFiles/TemplateModels/EIAAFreq.mdl
  223. lib/hyphy/TemplateBatchFiles/TemplateModels/EX.dat
  224. lib/hyphy/TemplateBatchFiles/TemplateModels/EX.mdl
  225. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/BLOSUM62
  226. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/Dayhoff
  227. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/H5N1
  228. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVBetween
  229. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVWithin
  230. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/IAV
  231. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/JTT
  232. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LCAP
  233. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LG
  234. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/MtArt
  235. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/VT
  236. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/WAG
  237. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/cpREV
  238. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/modellist.ibf
  239. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtMAM
  240. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtREV24
  241. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/rtREV
  242. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECM
  243. lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECMu
  244. lib/hyphy/TemplateBatchFiles/TemplateModels/F81.mdl
  245. lib/hyphy/TemplateBatchFiles/TemplateModels/F81_binary.mdl
  246. lib/hyphy/TemplateBatchFiles/TemplateModels/F84.mdl
  247. lib/hyphy/TemplateBatchFiles/TemplateModels/F84P.mdl
  248. lib/hyphy/TemplateBatchFiles/TemplateModels/GRM.mdl
  249. lib/hyphy/TemplateBatchFiles/TemplateModels/GY94.ibf
  250. lib/hyphy/TemplateBatchFiles/TemplateModels/GY94.mdl
  251. lib/hyphy/TemplateBatchFiles/TemplateModels/GY94customF3x4.mdl
  252. lib/hyphy/TemplateBatchFiles/TemplateModels/GY94w9.mdl
  253. lib/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween+F.mdl
  254. lib/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.ibf
  255. lib/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.mdl
  256. lib/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin+F.mdl
  257. lib/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.ibf
  258. lib/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.mdl
  259. lib/hyphy/TemplateBatchFiles/TemplateModels/HKY85.mdl
  260. lib/hyphy/TemplateBatchFiles/TemplateModels/JC69.mdl
  261. lib/hyphy/TemplateBatchFiles/TemplateModels/JC69_binary.mdl
  262. lib/hyphy/TemplateBatchFiles/TemplateModels/Jones.mdl
  263. lib/hyphy/TemplateBatchFiles/TemplateModels/Jones_F.mdl
  264. lib/hyphy/TemplateBatchFiles/TemplateModels/K2P.mdl
  265. lib/hyphy/TemplateBatchFiles/TemplateModels/K3ST.mdl
  266. lib/hyphy/TemplateBatchFiles/TemplateModels/LCAP.mdl
  267. lib/hyphy/TemplateBatchFiles/TemplateModels/MEC.mdl
  268. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94.mdl
  269. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94custom.mdl
  270. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94customCF3x4.mdl
  271. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94customF1x4.mdl
  272. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94customFreqs.mdl
  273. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAA.mdl
  274. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAF61.mdl
  275. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAF61multiple.mdl
  276. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAFreqs.mdl
  277. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAUserFreqs.mdl
  278. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94wEX.mdl
  279. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94with9freqs.mdl
  280. lib/hyphy/TemplateBatchFiles/TemplateModels/MG94x2.mdl
  281. lib/hyphy/TemplateBatchFiles/TemplateModels/MGFreqsEstimator.ibf
  282. lib/hyphy/TemplateBatchFiles/TemplateModels/MGwAA.ibf
  283. lib/hyphy/TemplateBatchFiles/TemplateModels/MGwEX.ibf
  284. lib/hyphy/TemplateBatchFiles/TemplateModels/NRM+Freqs.mdl
  285. lib/hyphy/TemplateBatchFiles/TemplateModels/NRM.mdl
  286. lib/hyphy/TemplateBatchFiles/TemplateModels/PCH
  287. lib/hyphy/TemplateBatchFiles/TemplateModels/RNA16.mdl
  288. lib/hyphy/TemplateBatchFiles/TemplateModels/RNA16A
  289. lib/hyphy/TemplateBatchFiles/TemplateModels/RNA16SvH.mdl
  290. lib/hyphy/TemplateBatchFiles/TemplateModels/RNAEqualInput
  291. lib/hyphy/TemplateBatchFiles/TemplateModels/RNAF81
  292. lib/hyphy/TemplateBatchFiles/TemplateModels/RNAMuse95.mdl
  293. lib/hyphy/TemplateBatchFiles/TemplateModels/RNAREV
  294. lib/hyphy/TemplateBatchFiles/TemplateModels/RNAREV_1
  295. lib/hyphy/TemplateBatchFiles/TemplateModels/S4
  296. lib/hyphy/TemplateBatchFiles/TemplateModels/STGRM.mdl
  297. lib/hyphy/TemplateBatchFiles/TemplateModels/TrN.mdl
  298. lib/hyphy/TemplateBatchFiles/TemplateModels/UniversalCode.def
  299. lib/hyphy/TemplateBatchFiles/TemplateModels/WAG.mdl
  300. lib/hyphy/TemplateBatchFiles/TemplateModels/WAG_F.mdl
  301. lib/hyphy/TemplateBatchFiles/TemplateModels/Yang2000Distributions.def
  302. lib/hyphy/TemplateBatchFiles/TemplateModels/chooseGeneticCode.def
  303. lib/hyphy/TemplateBatchFiles/TemplateModels/custm4x4.mdl
  304. lib/hyphy/TemplateBatchFiles/TemplateModels/defineGamma.mdl
  305. lib/hyphy/TemplateBatchFiles/TemplateModels/defineHM.mdl
  306. lib/hyphy/TemplateBatchFiles/TemplateModels/fitness.mdl
  307. lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters.mdl
  308. lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters2.mdl
  309. lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters3.mdl
  310. lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters4.mdl
  311. lib/hyphy/TemplateBatchFiles/TemplateModels/modelParameters5.mdl
  312. lib/hyphy/TemplateBatchFiles/TemplateModels/models.lst
  313. lib/hyphy/TemplateBatchFiles/TemplateModels/mtMAM.mdl
  314. lib/hyphy/TemplateBatchFiles/TemplateModels/mtMAM_F.mdl
  315. lib/hyphy/TemplateBatchFiles/TemplateModels/mtREV.mdl
  316. lib/hyphy/TemplateBatchFiles/TemplateModels/mtREV_24.mdl
  317. lib/hyphy/TemplateBatchFiles/TemplateModels/mtREV_24_F.mdl
  318. lib/hyphy/TemplateBatchFiles/TemplateModels/reducedREV.mdl
  319. lib/hyphy/TemplateBatchFiles/TemplateModels/rtREV.mdl
  320. lib/hyphy/TemplateBatchFiles/TemplateModels/rtREV_F.mdl
  321. lib/hyphy/TemplateBatchFiles/TestBranchDNDS.bf
  322. lib/hyphy/TemplateBatchFiles/TestClade.bf
  323. lib/hyphy/TemplateBatchFiles/TestCladeMeans.bf
  324. lib/hyphy/TemplateBatchFiles/TopologySearch.bf
  325. lib/hyphy/TemplateBatchFiles/TopologySearchConstrained.bf
  326. lib/hyphy/TemplateBatchFiles/TreeCorrelationCoefficients.bf
  327. lib/hyphy/TemplateBatchFiles/TreeTools.ibf
  328. lib/hyphy/TemplateBatchFiles/UpperBound.bf
  329. lib/hyphy/TemplateBatchFiles/Utility/AncestralMapper.bf
  330. lib/hyphy/TemplateBatchFiles/Utility/BranchLengthFitters.bf
  331. lib/hyphy/TemplateBatchFiles/Utility/CoalescentPostProcessor.bf
  332. lib/hyphy/TemplateBatchFiles/Utility/CodonTools.bf
  333. lib/hyphy/TemplateBatchFiles/Utility/DBTools.ibf
  334. lib/hyphy/TemplateBatchFiles/Utility/DescriptiveStatistics.bf
  335. lib/hyphy/TemplateBatchFiles/Utility/GrabBag.bf
  336. lib/hyphy/TemplateBatchFiles/Utility/HXB2Mapper.bf
  337. lib/hyphy/TemplateBatchFiles/Utility/LocalMGREV.bf
  338. lib/hyphy/TemplateBatchFiles/Utility/LocalMGREVMLFreqs.bf
  339. lib/hyphy/TemplateBatchFiles/Utility/MPITools.bf
  340. lib/hyphy/TemplateBatchFiles/Utility/NJ.bf
  341. lib/hyphy/TemplateBatchFiles/Utility/PS_Plotters.bf
  342. lib/hyphy/TemplateBatchFiles/Utility/PostScript.bf
  343. lib/hyphy/TemplateBatchFiles/Utility/ProbabilityDistributions.bf
  344. lib/hyphy/TemplateBatchFiles/Utility/ReadDelimitedFiles.bf
  345. lib/hyphy/TemplateBatchFiles/Utility/TreeFunctions.bf
  346. lib/hyphy/TemplateBatchFiles/Utility/WriteDelimitedFiles.bf
  347. lib/hyphy/TemplateBatchFiles/WANC.bf
  348. lib/hyphy/TemplateBatchFiles/YangNielsenBranchSite2005.bf
  349. lib/hyphy/TemplateBatchFiles/_BMS_Aux.ibf
  350. lib/hyphy/TemplateBatchFiles/_CMS_Aux.ibf
  351. lib/hyphy/TemplateBatchFiles/_MFReader_.ibf
  352. lib/hyphy/TemplateBatchFiles/_tipDater.ibf
  353. lib/hyphy/TemplateBatchFiles/bayesgraph.ibf
  354. lib/hyphy/TemplateBatchFiles/binomial.ibf
  355. lib/hyphy/TemplateBatchFiles/branchSwappingFunctions.bf
  356. lib/hyphy/TemplateBatchFiles/categoryEcho.bf
  357. lib/hyphy/TemplateBatchFiles/chooseDistanceFormula.def
  358. lib/hyphy/TemplateBatchFiles/dNdSBivariateRateAnalysis.bf
  359. lib/hyphy/TemplateBatchFiles/dNdSDistributionComparison.bf
  360. lib/hyphy/TemplateBatchFiles/dNdSRateAnalysis.bf
  361. lib/hyphy/TemplateBatchFiles/dNdSResultProcessor.bf
  362. lib/hyphy/TemplateBatchFiles/dSdNTreeTools.ibf
  363. lib/hyphy/TemplateBatchFiles/distanceMethodNPBootstrap.bf
  364. lib/hyphy/TemplateBatchFiles/distanceRMethodNPBootstrap.bf
  365. lib/hyphy/TemplateBatchFiles/doNNISwap.bf
  366. lib/hyphy/TemplateBatchFiles/doSPRSwap.bf
  367. lib/hyphy/TemplateBatchFiles/files.lst
  368. lib/hyphy/TemplateBatchFiles/globalChecker.ibf
  369. lib/hyphy/TemplateBatchFiles/heuristicMethodNPBootstrap.bf
  370. lib/hyphy/TemplateBatchFiles/last.date
  371. lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf
  372. lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
  373. lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
  374. lib/hyphy/TemplateBatchFiles/libv3/convenience/math.bf
  375. lib/hyphy/TemplateBatchFiles/libv3/convenience/matrix.bf
  376. lib/hyphy/TemplateBatchFiles/libv3/convenience/random.bf
  377. lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf
  378. lib/hyphy/TemplateBatchFiles/libv3/function-loader.bf
  379. lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf
  380. lib/hyphy/TemplateBatchFiles/libv3/models/DNA/GTR-MutSel.bf
  381. lib/hyphy/TemplateBatchFiles/libv3/models/DNA/GTR.bf
  382. lib/hyphy/TemplateBatchFiles/libv3/models/DNA/HKY85.bf
  383. lib/hyphy/TemplateBatchFiles/libv3/models/DNA/JC69.bf
  384. lib/hyphy/TemplateBatchFiles/libv3/models/binary.bf
  385. lib/hyphy/TemplateBatchFiles/libv3/models/binary/charbinary.bf
  386. lib/hyphy/TemplateBatchFiles/libv3/models/binary/empirical.bf
  387. lib/hyphy/TemplateBatchFiles/libv3/models/codon.bf
  388. lib/hyphy/TemplateBatchFiles/libv3/models/codon/BS_REL.bf
  389. lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV.bf
  390. lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV_MH.bf
  391. lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV_PROPERTIES.bf
  392. lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV_TRIP.bf
  393. lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf
  394. lib/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf
  395. lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf
  396. lib/hyphy/TemplateBatchFiles/libv3/models/protein.bf
  397. lib/hyphy/TemplateBatchFiles/libv3/models/protein/REV.bf
  398. lib/hyphy/TemplateBatchFiles/libv3/models/protein/empirical.bf
  399. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/HIV.ibf
  400. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/JC69.ibf
  401. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/JTT.ibf
  402. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/LG.ibf
  403. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/WAG.ibf
  404. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/gcpREV.ibf
  405. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/mt.ibf
  406. lib/hyphy/TemplateBatchFiles/libv3/models/protein/matrix2dict_aux.bf
  407. lib/hyphy/TemplateBatchFiles/libv3/models/rate_variation.bf
  408. lib/hyphy/TemplateBatchFiles/libv3/stats.bf
  409. lib/hyphy/TemplateBatchFiles/libv3/tasks/alignments.bf
  410. lib/hyphy/TemplateBatchFiles/libv3/tasks/ancestral.bf
  411. lib/hyphy/TemplateBatchFiles/libv3/tasks/bayesgraph.ibf
  412. lib/hyphy/TemplateBatchFiles/libv3/tasks/distances.bf
  413. lib/hyphy/TemplateBatchFiles/libv3/tasks/estimators.bf
  414. lib/hyphy/TemplateBatchFiles/libv3/tasks/genetic_code.bf
  415. lib/hyphy/TemplateBatchFiles/libv3/tasks/mpi.bf
  416. lib/hyphy/TemplateBatchFiles/libv3/tasks/trees.bf
  417. lib/hyphy/TemplateBatchFiles/molclockBootstrap.bf
  418. lib/hyphy/TemplateBatchFiles/pairwiseDistanceEstimator.ibf
  419. lib/hyphy/TemplateBatchFiles/pairwiseDistanceEstimatorCounter.ibf
  420. lib/hyphy/TemplateBatchFiles/partitionSequences.ibf
  421. lib/hyphy/TemplateBatchFiles/posteriors.ibf
  422. lib/hyphy/TemplateBatchFiles/qndhelper1.ibf
  423. lib/hyphy/TemplateBatchFiles/qndhelper1_mf.ibf
  424. lib/hyphy/TemplateBatchFiles/qndhelper2.ibf
  425. lib/hyphy/TemplateBatchFiles/qndhelper2_mf.ibf
  426. lib/hyphy/TemplateBatchFiles/qndhelper3.ibf
  427. lib/hyphy/TemplateBatchFiles/qndhelper4.ibf
  428. lib/hyphy/TemplateBatchFiles/queryTree.bf
  429. lib/hyphy/TemplateBatchFiles/readIndexFile.bf
  430. lib/hyphy/TemplateBatchFiles/relative_nucleotide_rates.bf
  431. lib/hyphy/TemplateBatchFiles/relrateBootstrap.bf
  432. lib/hyphy/TemplateBatchFiles/relratioBootstrap.bf
  433. lib/hyphy/TemplateBatchFiles/selectModelParameters.bf
  434. lib/hyphy/TemplateBatchFiles/simpleBootstrap.bf
  435. lib/hyphy/data/brown.nuc
  436. lib/hyphy/data/integrase_BDA.nex
  437. lib/hyphy/data/p51.aa
  438. lib/hyphy/data/p51.nex
Collapse this list.
Dependency lines:
  • hyphy>0:biology/hyphy
To install the port: cd /usr/ports/biology/hyphy/ && make install clean
To add the package: pkg install hyphy
PKGNAME: hyphy
Flavors: there is no flavor information for this port.
ONLY_FOR_ARCHS: amd64 i386
distinfo:

Dependencies
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

USES:

Master Sites:
  1. https://codeload.github.com/veg/hyphy/tar.gz/2.5.8?dummy=/

Number of commits found: 12

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
28 Mar 2020 12:27:11
Original commit files touched by this commit  2.5.8
Revision:529331
jrm search for other commits by this committer
biology/hyphy: Update to version 2.5.8

Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.8
20 Mar 2020 01:30:46
Original commit files touched by this commit  2.5.7
Revision:528753
jrm search for other commits by this committer
biology/hyphy: Update to version 2.5.7

Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.7
17 Mar 2020 18:17:16
Original commit files touched by this commit  2.5.6
Revision:528590
jrm search for other commits by this committer
biology/hyphy: Update to version 2.5.6

Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.6
02 Mar 2020 01:31:57
Original commit files touched by this commit  2.5.5
Revision:527606
jrm search for other commits by this committer
biology/hyphy: Update to version 2.5.5

Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.5
21 Feb 2020 12:22:17
Original commit files touched by this commit  2.5.4
Revision:526622
jrm search for other commits by this committer
biology/hyphy: Update to version 2.5.4

Upstream changes: https://github.com/veg/hyphy/releases
26 Jul 2019 20:46:57
Original commit files touched by this commit  2.3.14.16_2
Revision:507372
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
25 Dec 2018 20:25:40
Original commit files touched by this commit  2.3.14.16_1
Revision:488341
tcberner search for other commits by this committer
Change cmake default behaviour to outsource.

Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".

I tried to only set insource where explictely needed.

PR:		232038
Exp-run by:	antoine
12 Dec 2018 01:35:36
Original commit files touched by this commit  2.3.14.16_1
Revision:487272
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
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: 12

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