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Port details
hyphy Hypothesis testing using Phylogenies
2.5.61 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 View this port on Repology. pkg-fallout 2.5.58Version 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: 2024-05-16 16:08:06
Commit Hash: 6388152
License: MIT
WWW:
https://www.hyphy.org/
Description:
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (448 items)
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  1. /usr/local/share/licenses/hyphy-2.5.61/catalog.mk
  2. /usr/local/share/licenses/hyphy-2.5.61/LICENSE
  3. /usr/local/share/licenses/hyphy-2.5.61/MIT
  4. bin/hyphy
  5. share/hyphy/GeneticCodes/Alt_Yeast_Nuclear.cod
  6. share/hyphy/GeneticCodes/Ascidian_mtDNA.cod
  7. share/hyphy/GeneticCodes/Blepharisma_Nuclear.cod
  8. share/hyphy/GeneticCodes/Ciliate.cod
  9. share/hyphy/GeneticCodes/Echinoderm_mtDNA.cod
  10. share/hyphy/GeneticCodes/Euplotid_Nuclear.cod
  11. share/hyphy/GeneticCodes/Flatworm_mtDNA.cod
  12. share/hyphy/GeneticCodes/Invertebrate_mtDNA.cod
  13. share/hyphy/GeneticCodes/Mold_mtDNA.cod
  14. share/hyphy/GeneticCodes/Thraustochytrium_mtDNA.cod
  15. share/hyphy/GeneticCodes/Vertebratemtdna.cod
  16. share/hyphy/GeneticCodes/Yeast_mtDNA.cod
  17. share/hyphy/SubstitutionClasses/AAEFV/Equal
  18. share/hyphy/SubstitutionClasses/AAEFV/Estimated
  19. share/hyphy/SubstitutionClasses/AAEFV/Observed In Data Set
  20. share/hyphy/SubstitutionClasses/AAEFV/Observed In Partition
  21. share/hyphy/SubstitutionClasses/CodonEFV/Equal
  22. share/hyphy/SubstitutionClasses/CodonEFV/Observed Codon
  23. share/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 3 params.
  24. share/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 9 params.
  25. share/hyphy/SubstitutionClasses/Heterogeneity/2 Bin Discrete
  26. share/hyphy/SubstitutionClasses/Heterogeneity/Beta
  27. share/hyphy/SubstitutionClasses/Heterogeneity/Beta-Gamma
  28. share/hyphy/SubstitutionClasses/Heterogeneity/General Discrete
  29. share/hyphy/SubstitutionClasses/Heterogeneity/Half Normal
  30. share/hyphy/SubstitutionClasses/Heterogeneity/Lognormal
  31. share/hyphy/SubstitutionClasses/NucEFV/Equal
  32. share/hyphy/SubstitutionClasses/NucEFV/Estimated
  33. share/hyphy/SubstitutionClasses/NucEFV/Observed In Data Set
  34. share/hyphy/SubstitutionClasses/NucEFV/Observed In Partition
  35. share/hyphy/SubstitutionClasses/aa.bf
  36. share/hyphy/SubstitutionClasses/codon.bf
  37. share/hyphy/SubstitutionClasses/dinuc.bf
  38. share/hyphy/SubstitutionClasses/nuc.bf
  39. share/hyphy/SubstitutionModels/Aminoacid/Dayhoff.mdl
  40. share/hyphy/SubstitutionModels/Aminoacid/EIAA.mdl
  41. share/hyphy/SubstitutionModels/Aminoacid/Fitness.mdl
  42. share/hyphy/SubstitutionModels/Aminoacid/Jones.mdl
  43. share/hyphy/SubstitutionModels/Aminoacid/mtREV.mdl
  44. share/hyphy/SubstitutionModels/Binary/F81.mdl
  45. share/hyphy/SubstitutionModels/Codon/GY94_3x4.mdl
  46. share/hyphy/SubstitutionModels/Codon/Lineage_MG94xHKY85.mdl
  47. share/hyphy/SubstitutionModels/Codon/MG94.mdl
  48. share/hyphy/SubstitutionModels/Codon/MG94REVOmegaCF3x4.mdl
  49. share/hyphy/SubstitutionModels/Codon/MG94_3x4.mdl
  50. share/hyphy/SubstitutionModels/Codon/MG94_HKY85x3_4.mdl
  51. share/hyphy/SubstitutionModels/Codon/MG94_REV_3x4.mdl
  52. share/hyphy/SubstitutionModels/Codon/MG94xHKY85_3x4_2Rates.mdl
  53. share/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV.mdl
  54. share/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV_GDD.mdl
  55. share/hyphy/SubstitutionModels/Codon/MG94xTN93_3x4.mdl
  56. share/hyphy/SubstitutionModels/Nucleotide/EFVEstimated.ibf
  57. share/hyphy/SubstitutionModels/Nucleotide/F81.mdl
  58. share/hyphy/SubstitutionModels/Nucleotide/HKY85.mdl
  59. share/hyphy/SubstitutionModels/Nucleotide/REV.mdl
  60. share/hyphy/SubstitutionModels/Nucleotide/REVBetaGamma.mdl
  61. share/hyphy/SubstitutionModels/Nucleotide/TrN.mdl
  62. share/hyphy/SubstitutionModels/User/Nucleotide/JC69
  63. share/hyphy/SubstitutionModels/User/Nucleotide/K2P
  64. share/hyphy/TemplateBatchFiles/2RatesAnalyses/GY94.mdl
  65. share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94GY94xREV_PARRIS_syn3.mdl
  66. share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREV.mdl
  67. share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate.mdl
  68. share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate_Multirate.mdl
  69. share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M1.def
  70. share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M2.def
  71. share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M3.def
  72. share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_syn3.def
  73. share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_synvar.def
  74. share/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGenerator.bf
  75. share/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGeneratorNoPS.bf
  76. share/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma1.def
  77. share/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2+Inv.def
  78. share/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2.def
  79. share/hyphy/TemplateBatchFiles/AAModelComparison.bf
  80. share/hyphy/TemplateBatchFiles/AddABias.ibf
  81. share/hyphy/TemplateBatchFiles/AnalyzeCodonData.bf
  82. share/hyphy/TemplateBatchFiles/AnalyzeDiNucData.bf
  83. share/hyphy/TemplateBatchFiles/AnalyzeNucDataFreq.bf
  84. share/hyphy/TemplateBatchFiles/AnalyzeNucProtData.bf
  85. share/hyphy/TemplateBatchFiles/BGM.bf
  86. share/hyphy/TemplateBatchFiles/BivariateCodonRateAnalysis.bf
  87. share/hyphy/TemplateBatchFiles/BranchSiteREL.bf
  88. share/hyphy/TemplateBatchFiles/BranchSiteRELMultiModel.bf
  89. share/hyphy/TemplateBatchFiles/CleanGaps.bf
  90. share/hyphy/TemplateBatchFiles/CleanStopCodons.bf
  91. share/hyphy/TemplateBatchFiles/ClusterAnalysis.bf
  92. share/hyphy/TemplateBatchFiles/ClusterByDistanceRange.bf
  93. share/hyphy/TemplateBatchFiles/CodonBivariateRateProcessor.bf
  94. share/hyphy/TemplateBatchFiles/CodonModelCompare.bf
  95. share/hyphy/TemplateBatchFiles/CodonToProtein.bf
  96. share/hyphy/TemplateBatchFiles/ConvertDataFile.bf
  97. share/hyphy/TemplateBatchFiles/DirectionalREL.bf
  98. share/hyphy/TemplateBatchFiles/DistanceMatrix.bf
  99. share/hyphy/TemplateBatchFiles/Distances/CodonTools.def
  100. share/hyphy/TemplateBatchFiles/Distances/CodonTools2.def
  101. share/hyphy/TemplateBatchFiles/Distances/CodonToolsMain.def
  102. share/hyphy/TemplateBatchFiles/Distances/JC69
  103. share/hyphy/TemplateBatchFiles/Distances/K2P
  104. share/hyphy/TemplateBatchFiles/Distances/K2P_RV
  105. share/hyphy/TemplateBatchFiles/Distances/Modified_Nei_Gojobori
  106. share/hyphy/TemplateBatchFiles/Distances/Nei_Gojobori
  107. share/hyphy/TemplateBatchFiles/Distances/PC
  108. share/hyphy/TemplateBatchFiles/Distances/PC_MH
  109. share/hyphy/TemplateBatchFiles/Distances/PC_RV
  110. share/hyphy/TemplateBatchFiles/Distances/T3P
  111. share/hyphy/TemplateBatchFiles/Distances/TN84
  112. share/hyphy/TemplateBatchFiles/Distances/TN93
  113. share/hyphy/TemplateBatchFiles/Distances/TN93_RV
  114. share/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ
  115. share/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ_FR
  116. share/hyphy/TemplateBatchFiles/Distances/p_Distance
  117. share/hyphy/TemplateBatchFiles/Distances/p_Distance_aa
  118. share/hyphy/TemplateBatchFiles/Distances/p_Distance_binary
  119. share/hyphy/TemplateBatchFiles/Distances/p_Distance_codon
  120. share/hyphy/TemplateBatchFiles/F_ST.bf
  121. share/hyphy/TemplateBatchFiles/FitnessAAModels.bf
  122. share/hyphy/TemplateBatchFiles/GARD.bf
  123. share/hyphy/TemplateBatchFiles/GA_CHC.ibf
  124. share/hyphy/TemplateBatchFiles/GA_CHC_Binary.ibf
  125. share/hyphy/TemplateBatchFiles/GUI/crayolaColors.def
  126. share/hyphy/TemplateBatchFiles/Gateaux.bf
  127. share/hyphy/TemplateBatchFiles/GateauxMR.bf
  128. share/hyphy/TemplateBatchFiles/KHTest.bf
  129. share/hyphy/TemplateBatchFiles/LEISR.bf
  130. share/hyphy/TemplateBatchFiles/LHT.bf
  131. share/hyphy/TemplateBatchFiles/LRTRecombTest.bf
  132. share/hyphy/TemplateBatchFiles/LZ_Complexity.bf
  133. share/hyphy/TemplateBatchFiles/LocalMolClock.bf
  134. share/hyphy/TemplateBatchFiles/MGvsGY.bf
  135. share/hyphy/TemplateBatchFiles/MergeSequences.bf
  136. share/hyphy/TemplateBatchFiles/MergeSites.bf
  137. share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/BranchAPriori.bf
  138. share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/CountSubstitutions.bf
  139. share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/EffectOfTopology.bf
  140. share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/ErrorEstimates.bf
  141. share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/LRT.bf
  142. share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/LocalvsGlobal.bf
  143. share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/NeutralExpectation.bf
  144. share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/NucleotideBiases.bf
  145. share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/Phylohandbook.bf
  146. share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/WhatsInTheMean.bf
  147. share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/dSdN.bf
  148. share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/Drosophilia_adh.nex
  149. share/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/H5N1_HA_5.nex
  150. share/hyphy/TemplateBatchFiles/ModelTest.bf
  151. share/hyphy/TemplateBatchFiles/MolClockAllRoots.bf
  152. share/hyphy/TemplateBatchFiles/MolecularClock.bf
  153. share/hyphy/TemplateBatchFiles/MSS-joint-fitter.bf
  154. share/hyphy/TemplateBatchFiles/MSS-selector-2.bf
  155. share/hyphy/TemplateBatchFiles/MSS-selector.bf
  156. share/hyphy/TemplateBatchFiles/NeighborJoining.bf
  157. share/hyphy/TemplateBatchFiles/NielsenYang.bf
  158. share/hyphy/TemplateBatchFiles/NucModelCompare.bf
  159. share/hyphy/TemplateBatchFiles/PARRIS.bf
  160. share/hyphy/TemplateBatchFiles/PairwiseRelativeRate.bf
  161. share/hyphy/TemplateBatchFiles/PairwiseRelativeRatio.bf
  162. share/hyphy/TemplateBatchFiles/PartitionDataFile.bf
  163. share/hyphy/TemplateBatchFiles/ProteinAnalyses/ProteinGTRFit.bf
  164. share/hyphy/TemplateBatchFiles/ProteinAnalyses/ProteinGTRFit_helper.ibf
  165. share/hyphy/TemplateBatchFiles/ProteinAnalyses/README_relative_prot_rates.md
  166. share/hyphy/TemplateBatchFiles/ProteinAnalyses/plusF_helper.ibf
  167. share/hyphy/TemplateBatchFiles/ProteinAnalyses/relative_prot_rates.bf
  168. share/hyphy/TemplateBatchFiles/ReduceDataSetMatrix.bf
  169. share/hyphy/TemplateBatchFiles/RelativeRate.bf
  170. share/hyphy/TemplateBatchFiles/RelativeRatio.bf
  171. share/hyphy/TemplateBatchFiles/SGASimProcessor.bf
  172. share/hyphy/TemplateBatchFiles/SGEmulator.bf
  173. share/hyphy/TemplateBatchFiles/SGEmulator_MF.bf
  174. share/hyphy/TemplateBatchFiles/SGIvL.bf
  175. share/hyphy/TemplateBatchFiles/SM-2019.bf
  176. share/hyphy/TemplateBatchFiles/Samplers/lhc-ErrorEst.bf
  177. share/hyphy/TemplateBatchFiles/Samplers/lhc.bf
  178. share/hyphy/TemplateBatchFiles/Samplers/lhc_supp.ibf
  179. share/hyphy/TemplateBatchFiles/Samplers/sir.bf
  180. share/hyphy/TemplateBatchFiles/Samplers/srs-ErrorEst.ibf
  181. share/hyphy/TemplateBatchFiles/Samplers/srs.ibf
  182. share/hyphy/TemplateBatchFiles/SandNSAmbigs.bf
  183. share/hyphy/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf
  184. share/hyphy/TemplateBatchFiles/SelectionAnalyses/BranchSiteREL.bf
  185. share/hyphy/TemplateBatchFiles/SelectionAnalyses/FADE.bf
  186. share/hyphy/TemplateBatchFiles/SelectionAnalyses/FEL.bf
  187. share/hyphy/TemplateBatchFiles/SelectionAnalyses/FitMultiModel.bf
  188. share/hyphy/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf
  189. share/hyphy/TemplateBatchFiles/SelectionAnalyses/MEME.bf
  190. share/hyphy/TemplateBatchFiles/SelectionAnalyses/PRIME.bf
  191. share/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX-Groups.bf
  192. share/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX.bf
  193. share/hyphy/TemplateBatchFiles/SelectionAnalyses/SLAC.bf
  194. share/hyphy/TemplateBatchFiles/SelectionAnalyses/SingleOmega.bf
  195. share/hyphy/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf
  196. share/hyphy/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf
  197. share/hyphy/TemplateBatchFiles/SelectionAnalyses/contrast-meme.bf
  198. share/hyphy/TemplateBatchFiles/SelectionAnalyses/error-filter.bf
  199. share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/grid_compute.ibf
  200. share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf
  201. share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf
  202. share/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf
  203. share/hyphy/TemplateBatchFiles/SelectionLRT.bf
  204. share/hyphy/TemplateBatchFiles/SeqAlignShared.ibf
  205. share/hyphy/TemplateBatchFiles/SeqAlignmentCodon.bf
  206. share/hyphy/TemplateBatchFiles/SeqAlignmentCodonShared.ibf
  207. share/hyphy/TemplateBatchFiles/SeqAlignmentNucShared.ibf
  208. share/hyphy/TemplateBatchFiles/SequentialAddition.bf
  209. share/hyphy/TemplateBatchFiles/SequentialAddition.ibf
  210. share/hyphy/TemplateBatchFiles/SimilarityPlot.bf
  211. share/hyphy/TemplateBatchFiles/SimmondsAI.bf
  212. share/hyphy/TemplateBatchFiles/SingleBreakpointRecomb.bf
  213. share/hyphy/TemplateBatchFiles/SlidingWindowAnalysis.bf
  214. share/hyphy/TemplateBatchFiles/TemplateModels/190
  215. share/hyphy/TemplateBatchFiles/TemplateModels/BranchSiteTemplate.mdl
  216. share/hyphy/TemplateBatchFiles/TemplateModels/CF3x4.bf
  217. share/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA.mdl
  218. share/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA_empirical.mdl
  219. share/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff.mdl
  220. share/hyphy/TemplateBatchFiles/TemplateModels/Dayhoff_F.mdl
  221. share/hyphy/TemplateBatchFiles/TemplateModels/Default
  222. share/hyphy/TemplateBatchFiles/TemplateModels/ECM+F+omega.mdl
  223. share/hyphy/TemplateBatchFiles/TemplateModels/ECM+F.mdl
  224. share/hyphy/TemplateBatchFiles/TemplateModels/ECM+F3x4.mdl
  225. share/hyphy/TemplateBatchFiles/TemplateModels/ECM+MLFREQS.mdl
  226. share/hyphy/TemplateBatchFiles/TemplateModels/ECM.mdl
  227. share/hyphy/TemplateBatchFiles/TemplateModels/EIAA.mdl
  228. share/hyphy/TemplateBatchFiles/TemplateModels/EIAAFreq.mdl
  229. share/hyphy/TemplateBatchFiles/TemplateModels/EX.dat
  230. share/hyphy/TemplateBatchFiles/TemplateModels/EX.mdl
  231. share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/BLOSUM62
  232. share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/Dayhoff
  233. share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/H5N1
  234. share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVBetween
  235. share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVWithin
  236. share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/IAV
  237. share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/JTT
  238. share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LCAP
  239. share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LG
  240. share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/MtArt
  241. share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/VT
  242. share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/WAG
  243. share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/cpREV
  244. share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/modellist.ibf
  245. share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtMAM
  246. share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtREV24
  247. share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/rtREV
  248. share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECM
  249. share/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalCodon/KHG_ECMu
  250. share/hyphy/TemplateBatchFiles/TemplateModels/F81.mdl
  251. share/hyphy/TemplateBatchFiles/TemplateModels/F81_binary.mdl
  252. share/hyphy/TemplateBatchFiles/TemplateModels/F84.mdl
  253. share/hyphy/TemplateBatchFiles/TemplateModels/F84P.mdl
  254. share/hyphy/TemplateBatchFiles/TemplateModels/GRM.mdl
  255. share/hyphy/TemplateBatchFiles/TemplateModels/GY94.ibf
  256. share/hyphy/TemplateBatchFiles/TemplateModels/GY94.mdl
  257. share/hyphy/TemplateBatchFiles/TemplateModels/GY94customF3x4.mdl
  258. share/hyphy/TemplateBatchFiles/TemplateModels/GY94w9.mdl
  259. share/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween+F.mdl
  260. share/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.ibf
  261. share/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween.mdl
  262. share/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin+F.mdl
  263. share/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.ibf
  264. share/hyphy/TemplateBatchFiles/TemplateModels/HIVwithin.mdl
  265. share/hyphy/TemplateBatchFiles/TemplateModels/HKY85.mdl
  266. share/hyphy/TemplateBatchFiles/TemplateModels/JC69.mdl
  267. share/hyphy/TemplateBatchFiles/TemplateModels/JC69_binary.mdl
  268. share/hyphy/TemplateBatchFiles/TemplateModels/Jones.mdl
  269. share/hyphy/TemplateBatchFiles/TemplateModels/Jones_F.mdl
  270. share/hyphy/TemplateBatchFiles/TemplateModels/K2P.mdl
  271. share/hyphy/TemplateBatchFiles/TemplateModels/K3ST.mdl
  272. share/hyphy/TemplateBatchFiles/TemplateModels/LCAP.mdl
  273. share/hyphy/TemplateBatchFiles/TemplateModels/MEC.mdl
  274. share/hyphy/TemplateBatchFiles/TemplateModels/MG94.mdl
  275. share/hyphy/TemplateBatchFiles/TemplateModels/MG94custom.mdl
  276. share/hyphy/TemplateBatchFiles/TemplateModels/MG94customCF3x4.mdl
  277. share/hyphy/TemplateBatchFiles/TemplateModels/MG94customF1x4.mdl
  278. share/hyphy/TemplateBatchFiles/TemplateModels/MG94customFreqs.mdl
  279. share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAA.mdl
  280. share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAF61.mdl
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  283. share/hyphy/TemplateBatchFiles/TemplateModels/MG94wAAUserFreqs.mdl
  284. share/hyphy/TemplateBatchFiles/TemplateModels/MG94wEX.mdl
  285. share/hyphy/TemplateBatchFiles/TemplateModels/MG94with9freqs.mdl
  286. share/hyphy/TemplateBatchFiles/TemplateModels/MG94x2.mdl
  287. share/hyphy/TemplateBatchFiles/TemplateModels/MGFreqsEstimator.ibf
  288. share/hyphy/TemplateBatchFiles/TemplateModels/MGwAA.ibf
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  290. share/hyphy/TemplateBatchFiles/TemplateModels/NRM+Freqs.mdl
  291. share/hyphy/TemplateBatchFiles/TemplateModels/NRM.mdl
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  293. share/hyphy/TemplateBatchFiles/TemplateModels/RNA16.mdl
  294. share/hyphy/TemplateBatchFiles/TemplateModels/RNA16A
  295. share/hyphy/TemplateBatchFiles/TemplateModels/RNA16SvH.mdl
  296. share/hyphy/TemplateBatchFiles/TemplateModels/RNAEqualInput
  297. share/hyphy/TemplateBatchFiles/TemplateModels/RNAF81
  298. share/hyphy/TemplateBatchFiles/TemplateModels/RNAMuse95.mdl
  299. share/hyphy/TemplateBatchFiles/TemplateModels/RNAREV
  300. share/hyphy/TemplateBatchFiles/TemplateModels/RNAREV_1
  301. share/hyphy/TemplateBatchFiles/TemplateModels/S4
  302. share/hyphy/TemplateBatchFiles/TemplateModels/STGRM.mdl
  303. share/hyphy/TemplateBatchFiles/TemplateModels/TrN.mdl
  304. share/hyphy/TemplateBatchFiles/TemplateModels/UniversalCode.def
  305. share/hyphy/TemplateBatchFiles/TemplateModels/WAG.mdl
  306. share/hyphy/TemplateBatchFiles/TemplateModels/WAG_F.mdl
  307. share/hyphy/TemplateBatchFiles/TemplateModels/Yang2000Distributions.def
  308. share/hyphy/TemplateBatchFiles/TemplateModels/chooseGeneticCode.def
  309. share/hyphy/TemplateBatchFiles/TemplateModels/custm4x4.mdl
  310. share/hyphy/TemplateBatchFiles/TemplateModels/defineGamma.mdl
  311. share/hyphy/TemplateBatchFiles/TemplateModels/defineHM.mdl
  312. share/hyphy/TemplateBatchFiles/TemplateModels/fitness.mdl
  313. share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters.mdl
  314. share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters2.mdl
  315. share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters3.mdl
  316. share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters4.mdl
  317. share/hyphy/TemplateBatchFiles/TemplateModels/modelParameters5.mdl
  318. share/hyphy/TemplateBatchFiles/TemplateModels/models.lst
  319. share/hyphy/TemplateBatchFiles/TemplateModels/mtMAM.mdl
  320. share/hyphy/TemplateBatchFiles/TemplateModels/mtMAM_F.mdl
  321. share/hyphy/TemplateBatchFiles/TemplateModels/mtREV.mdl
  322. share/hyphy/TemplateBatchFiles/TemplateModels/mtREV_24.mdl
  323. share/hyphy/TemplateBatchFiles/TemplateModels/mtREV_24_F.mdl
  324. share/hyphy/TemplateBatchFiles/TemplateModels/reducedREV.mdl
  325. share/hyphy/TemplateBatchFiles/TemplateModels/rtREV.mdl
  326. share/hyphy/TemplateBatchFiles/TemplateModels/rtREV_F.mdl
  327. share/hyphy/TemplateBatchFiles/TestBranchDNDS.bf
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  329. share/hyphy/TemplateBatchFiles/TestCladeMeans.bf
  330. share/hyphy/TemplateBatchFiles/TopologySearch.bf
  331. share/hyphy/TemplateBatchFiles/TopologySearchConstrained.bf
  332. share/hyphy/TemplateBatchFiles/TreeCorrelationCoefficients.bf
  333. share/hyphy/TemplateBatchFiles/TreeTools.ibf
  334. share/hyphy/TemplateBatchFiles/UpperBound.bf
  335. share/hyphy/TemplateBatchFiles/Utility/AncestralMapper.bf
  336. share/hyphy/TemplateBatchFiles/Utility/BranchLengthFitters.bf
  337. share/hyphy/TemplateBatchFiles/Utility/CoalescentPostProcessor.bf
  338. share/hyphy/TemplateBatchFiles/Utility/CodonTools.bf
  339. share/hyphy/TemplateBatchFiles/Utility/DBTools.ibf
  340. share/hyphy/TemplateBatchFiles/Utility/DescriptiveStatistics.bf
  341. share/hyphy/TemplateBatchFiles/Utility/GrabBag.bf
  342. share/hyphy/TemplateBatchFiles/Utility/HXB2Mapper.bf
  343. share/hyphy/TemplateBatchFiles/Utility/LocalMGREV.bf
  344. share/hyphy/TemplateBatchFiles/Utility/LocalMGREVMLFreqs.bf
  345. share/hyphy/TemplateBatchFiles/Utility/MPITools.bf
  346. share/hyphy/TemplateBatchFiles/Utility/NJ.bf
  347. share/hyphy/TemplateBatchFiles/Utility/PS_Plotters.bf
  348. share/hyphy/TemplateBatchFiles/Utility/PostScript.bf
  349. share/hyphy/TemplateBatchFiles/Utility/ProbabilityDistributions.bf
  350. share/hyphy/TemplateBatchFiles/Utility/ReadDelimitedFiles.bf
  351. share/hyphy/TemplateBatchFiles/Utility/TreeFunctions.bf
  352. share/hyphy/TemplateBatchFiles/Utility/WriteDelimitedFiles.bf
  353. share/hyphy/TemplateBatchFiles/WANC.bf
  354. share/hyphy/TemplateBatchFiles/YangNielsenBranchSite2005.bf
  355. share/hyphy/TemplateBatchFiles/_BMS_Aux.ibf
  356. share/hyphy/TemplateBatchFiles/_CMS_Aux.ibf
  357. share/hyphy/TemplateBatchFiles/_MFReader_.ibf
  358. share/hyphy/TemplateBatchFiles/_tipDater.ibf
  359. share/hyphy/TemplateBatchFiles/bayesgraph.ibf
  360. share/hyphy/TemplateBatchFiles/binomial.ibf
  361. share/hyphy/TemplateBatchFiles/branchSwappingFunctions.bf
  362. share/hyphy/TemplateBatchFiles/categoryEcho.bf
  363. share/hyphy/TemplateBatchFiles/chooseDistanceFormula.def
  364. share/hyphy/TemplateBatchFiles/dNdSBivariateRateAnalysis.bf
  365. share/hyphy/TemplateBatchFiles/dNdSDistributionComparison.bf
  366. share/hyphy/TemplateBatchFiles/dNdSRateAnalysis.bf
  367. share/hyphy/TemplateBatchFiles/dNdSResultProcessor.bf
  368. share/hyphy/TemplateBatchFiles/dSdNTreeTools.ibf
  369. share/hyphy/TemplateBatchFiles/distanceMethodNPBootstrap.bf
  370. share/hyphy/TemplateBatchFiles/distanceRMethodNPBootstrap.bf
  371. share/hyphy/TemplateBatchFiles/doNNISwap.bf
  372. share/hyphy/TemplateBatchFiles/doSPRSwap.bf
  373. share/hyphy/TemplateBatchFiles/files.lst
  374. share/hyphy/TemplateBatchFiles/globalChecker.ibf
  375. share/hyphy/TemplateBatchFiles/heuristicMethodNPBootstrap.bf
  376. share/hyphy/TemplateBatchFiles/last.date
  377. share/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf
  378. share/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
  379. share/hyphy/TemplateBatchFiles/libv3/all-terms.bf
  380. share/hyphy/TemplateBatchFiles/libv3/convenience/math.bf
  381. share/hyphy/TemplateBatchFiles/libv3/convenience/matrix.bf
  382. share/hyphy/TemplateBatchFiles/libv3/convenience/random.bf
  383. share/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf
  384. share/hyphy/TemplateBatchFiles/libv3/function-loader.bf
  385. share/hyphy/TemplateBatchFiles/libv3/models/DNA.bf
  386. share/hyphy/TemplateBatchFiles/libv3/models/DNA/GTR-MutSel.bf
  387. share/hyphy/TemplateBatchFiles/libv3/models/DNA/GTR.bf
  388. share/hyphy/TemplateBatchFiles/libv3/models/DNA/HKY85.bf
  389. share/hyphy/TemplateBatchFiles/libv3/models/DNA/JC69.bf
  390. share/hyphy/TemplateBatchFiles/libv3/models/binary.bf
  391. share/hyphy/TemplateBatchFiles/libv3/models/binary/charbinary.bf
  392. share/hyphy/TemplateBatchFiles/libv3/models/binary/empirical.bf
  393. share/hyphy/TemplateBatchFiles/libv3/models/codon.bf
  394. share/hyphy/TemplateBatchFiles/libv3/models/codon/BS_REL.bf
  395. share/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV.bf
  396. share/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV_MH.bf
  397. share/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV_PROPERTIES.bf
  398. share/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV_TRIP.bf
  399. share/hyphy/TemplateBatchFiles/libv3/models/codon/MSS.bf
  400. share/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf
  401. share/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf
  402. share/hyphy/TemplateBatchFiles/libv3/models/parameters.bf
  403. share/hyphy/TemplateBatchFiles/libv3/models/protein.bf
  404. share/hyphy/TemplateBatchFiles/libv3/models/protein/REV.bf
  405. share/hyphy/TemplateBatchFiles/libv3/models/protein/empirical.bf
  406. share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/HIV.ibf
  407. share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/JC69.ibf
  408. share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/JTT.ibf
  409. share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/LG.ibf
  410. share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/WAG.ibf
  411. share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/gcpREV.ibf
  412. share/hyphy/TemplateBatchFiles/libv3/models/protein/matrices/mt.ibf
  413. share/hyphy/TemplateBatchFiles/libv3/models/protein/matrix2dict_aux.bf
  414. share/hyphy/TemplateBatchFiles/libv3/models/rate_variation.bf
  415. share/hyphy/TemplateBatchFiles/libv3/stats.bf
  416. share/hyphy/TemplateBatchFiles/libv3/tasks/alignments.bf
  417. share/hyphy/TemplateBatchFiles/libv3/tasks/ancestral.bf
  418. share/hyphy/TemplateBatchFiles/libv3/tasks/bayesgraph.ibf
  419. share/hyphy/TemplateBatchFiles/libv3/tasks/distances.bf
  420. share/hyphy/TemplateBatchFiles/libv3/tasks/estimators.bf
  421. share/hyphy/TemplateBatchFiles/libv3/tasks/genetic_code.bf
  422. share/hyphy/TemplateBatchFiles/libv3/tasks/mpi.bf
  423. share/hyphy/TemplateBatchFiles/libv3/tasks/trees.bf
  424. share/hyphy/TemplateBatchFiles/molclockBootstrap.bf
  425. share/hyphy/TemplateBatchFiles/pairwiseDistanceEstimator.ibf
  426. share/hyphy/TemplateBatchFiles/pairwiseDistanceEstimatorCounter.ibf
  427. share/hyphy/TemplateBatchFiles/partitionSequences.ibf
  428. share/hyphy/TemplateBatchFiles/posteriors.ibf
  429. share/hyphy/TemplateBatchFiles/qndhelper1.ibf
  430. share/hyphy/TemplateBatchFiles/qndhelper1_mf.ibf
  431. share/hyphy/TemplateBatchFiles/qndhelper2.ibf
  432. share/hyphy/TemplateBatchFiles/qndhelper2_mf.ibf
  433. share/hyphy/TemplateBatchFiles/qndhelper3.ibf
  434. share/hyphy/TemplateBatchFiles/qndhelper4.ibf
  435. share/hyphy/TemplateBatchFiles/queryTree.bf
  436. share/hyphy/TemplateBatchFiles/readIndexFile.bf
  437. share/hyphy/TemplateBatchFiles/relative_nucleotide_rates.bf
  438. share/hyphy/TemplateBatchFiles/relrateBootstrap.bf
  439. share/hyphy/TemplateBatchFiles/relratioBootstrap.bf
  440. share/hyphy/TemplateBatchFiles/selectModelParameters.bf
  441. share/hyphy/TemplateBatchFiles/simpleBootstrap.bf
  442. share/hyphy/data/brown.nuc
  443. share/hyphy/data/integrase_BDA.nex
  444. share/hyphy/data/p51.aa
  445. share/hyphy/data/p51.nex
  446. @owner
  447. @group
  448. @mode
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, run one of these commands:
  • pkg install biology/hyphy
  • pkg install hyphy
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: hyphy
Flavors: there is no flavor information for this port.
ONLY_FOR_ARCHS: aarch64 amd64 i386 powerpc powerpc64 powerpc64le
distinfo:
TIMESTAMP = 1715871637 SHA256 (veg-hyphy-2.5.61_GH0.tar.gz) = 5a470ad64e9ea53296d87e69298ab2354d563338a9ec05b529679c42e23b3025 SIZE (veg-hyphy-2.5.61_GH0.tar.gz) = 5604227

Packages (timestamps in pop-ups are UTC):
hyphy
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.5.602.5.61--2.5.61---
FreeBSD:13:quarterly2.5.582.5.58--2.5.582.5.582.5.582.5.58
FreeBSD:14:latest2.5.602.5.60--2.5.61--2.5.51.h
FreeBSD:14:quarterly2.5.582.5.58--2.5.582.5.582.5.582.5.58
FreeBSD:15:latest2.5.602.5.61n/a-n/a2.5.582.5.582.5.58
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. cmake : devel/cmake-core
  2. ninja : devel/ninja
Test dependencies:
  1. bash : shells/bash
Library dependencies:
  1. libcurl.so : ftp/curl
There are no ports dependent upon this port

Configuration Options:
===> The following configuration options are available for hyphy-2.5.61: AVX=off: Advanced vector extensions support ===> Use 'make config' to modify these settings
Options name:
biology_hyphy
USES:
cmake:insource,testing localbase:ldflags
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/veg/hyphy/tar.gz/2.5.61?dummy=/
Collapse this list.

Number of commits found: 68

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.5.61
16 May 2024 16:08:06
commit hash: 6388152516ca19c44dc4bf6bcf54e428127d34c9commit hash: 6388152516ca19c44dc4bf6bcf54e428127d34c9commit hash: 6388152516ca19c44dc4bf6bcf54e428127d34c9commit hash: 6388152516ca19c44dc4bf6bcf54e428127d34c9 files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.5.61

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.61
Commit log:	https://github.com/veg/hyphy/compare/2.5.56...2.5.61
Sponsored by:	The FreeBSD Foundation
2.5.60
14 Apr 2024 21:14:19
commit hash: ce15321ea97ee0345f2ace3dd24b6ee87473a901commit hash: ce15321ea97ee0345f2ace3dd24b6ee87473a901commit hash: ce15321ea97ee0345f2ace3dd24b6ee87473a901commit hash: ce15321ea97ee0345f2ace3dd24b6ee87473a901 files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.5.60

Changes:	https://github.com/veg/hyphy/compare/2.5.59...2.5.60
		https://github.com/veg/hyphy/compare/2.5.58...2.5.59
Sponsored by:	The FreeBSD Foundation
2.5.58
23 Dec 2023 17:28:25
commit hash: 3b90027c760a3591b2757fab96ab0e04298c62a9commit hash: 3b90027c760a3591b2757fab96ab0e04298c62a9commit hash: 3b90027c760a3591b2757fab96ab0e04298c62a9commit hash: 3b90027c760a3591b2757fab96ab0e04298c62a9 files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.5.58

Changes:	https://github.com/veg/hyphy/releases/tag/2.5.58
Sponsored by:	The FreeBSD Foundation
2.5.57
15 Nov 2023 00:09:46
commit hash: 0bb4adb204cd139bddf73dd5e02560d41df648b3commit hash: 0bb4adb204cd139bddf73dd5e02560d41df648b3commit hash: 0bb4adb204cd139bddf73dd5e02560d41df648b3commit hash: 0bb4adb204cd139bddf73dd5e02560d41df648b3 files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.5.57

Changes:	https://github.com/veg/hyphy/releases/tag/2.5.57
Sponsored by:	The FreeBSD Foundation
2.5.56
07 Nov 2023 14:46:41
commit hash: 82a2407a5c48f710fc283bc847ca717245cb8a2ccommit hash: 82a2407a5c48f710fc283bc847ca717245cb8a2ccommit hash: 82a2407a5c48f710fc283bc847ca717245cb8a2ccommit hash: 82a2407a5c48f710fc283bc847ca717245cb8a2c files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.5.56

Changes:	https://github.com/veg/hyphy/releases/tag/2.5.56
                https://github.com/veg/hyphy/releases/tag/2.5.55
Sponsored by:	The FreeBSD Foundation
2.5.53
05 Sep 2023 14:49:35
commit hash: 5d6c87d761c758963978c3b9ee532b87ecdef824commit hash: 5d6c87d761c758963978c3b9ee532b87ecdef824commit hash: 5d6c87d761c758963978c3b9ee532b87ecdef824commit hash: 5d6c87d761c758963978c3b9ee532b87ecdef824 files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.5.53

Changes:	https://github.com/veg/hyphy/releases/tag/2.5.53
Sponsored by:	The FreeBSD Foundation
2.5.52
09 Aug 2023 17:39:17
commit hash: 8d0b7976cd078892b48202aa8acc0810135bf02acommit hash: 8d0b7976cd078892b48202aa8acc0810135bf02acommit hash: 8d0b7976cd078892b48202aa8acc0810135bf02acommit hash: 8d0b7976cd078892b48202aa8acc0810135bf02a files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.5.52

- FEL test is now passing, so remove comment about it failing.
- Remove armv7 support since most tests are segfaulting.

Changes:	https://github.com/veg/hyphy/releases/tag/2.5.52
Sponsored by:	The FreeBSD Foundation
Differential Revision: https://reviews.freebsd.org/D41393
Tested by:	fuz (armv7)
2.5.51.h
30 Jun 2023 12:00:28
commit hash: b27d05a94c645a3ba02c50122a229c37bec42559commit hash: b27d05a94c645a3ba02c50122a229c37bec42559commit hash: b27d05a94c645a3ba02c50122a229c37bec42559commit hash: b27d05a94c645a3ba02c50122a229c37bec42559 files touched by this commit
Robert Clausecker (fuz) search for other commits by this committer
biology/hyphy: fix build on armv7

With OpenMP not present, the code had a duplicate function definition.
Get rid of one of the two to enable a build on armv7.

Approved by:	portmgr (build fix blanket)
2.5.51.h
29 May 2023 00:09:56
commit hash: 5a78e2be917576be30b49e341a5e2a0a4b4a11b5commit hash: 5a78e2be917576be30b49e341a5e2a0a4b4a11b5commit hash: 5a78e2be917576be30b49e341a5e2a0a4b4a11b5commit hash: 5a78e2be917576be30b49e341a5e2a0a4b4a11b5 files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.5.51hf

FEL test still fails.  See https://github.com/veg/hyphy/issues/1585.

Sponsored by:	The FreeBSD Foundation
2.5.50
19 Apr 2023 16:30:57
commit hash: 947a366e110c02f686746b8dd3468e1ff2d8e2a9commit hash: 947a366e110c02f686746b8dd3468e1ff2d8e2a9commit hash: 947a366e110c02f686746b8dd3468e1ff2d8e2a9commit hash: 947a366e110c02f686746b8dd3468e1ff2d8e2a9 files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.5.50

This release fixes a bug when not using openmp.
https://github.com/veg/hyphy/compare/2.5.49...2.5.50

Sponsored by:	The FreeBSD Foundation
2.5.49
24 Mar 2023 15:54:30
commit hash: 68b8e0027d365f2e5f8085f6cc820bc78524c7becommit hash: 68b8e0027d365f2e5f8085f6cc820bc78524c7becommit hash: 68b8e0027d365f2e5f8085f6cc820bc78524c7becommit hash: 68b8e0027d365f2e5f8085f6cc820bc78524c7be files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.5.49

Sponsored by:	The FreeBSD Foundation
2.5.48
05 Mar 2023 15:51:37
commit hash: 99d4dc3c2bb986c76cc293d3d372b3d5e2cc19bbcommit hash: 99d4dc3c2bb986c76cc293d3d372b3d5e2cc19bbcommit hash: 99d4dc3c2bb986c76cc293d3d372b3d5e2cc19bbcommit hash: 99d4dc3c2bb986c76cc293d3d372b3d5e2cc19bb files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.5.48

Changes:	https://github.com/veg/hyphy/releases/tag/2.5.48
Sponsored by:	The FreeBSD Foundation
2.5.47
04 Feb 2023 03:36:47
commit hash: 048831ec575bed26387643f1d44fc4f6a7bbdb83commit hash: 048831ec575bed26387643f1d44fc4f6a7bbdb83commit hash: 048831ec575bed26387643f1d44fc4f6a7bbdb83commit hash: 048831ec575bed26387643f1d44fc4f6a7bbdb83 files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.5.47

Changes:	https://github.com/veg/hyphy/releases/tag/2.5.47
Sponsored by:	The FreeBSD Foundation
2.5.46.h1
10 Jan 2023 02:05:57
commit hash: c6a8b4ea40e092f95f6386c79972b4aa95ef7387commit hash: c6a8b4ea40e092f95f6386c79972b4aa95ef7387commit hash: c6a8b4ea40e092f95f6386c79972b4aa95ef7387commit hash: c6a8b4ea40e092f95f6386c79972b4aa95ef7387 files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to upstream tag 2.5.46hf1

Sponsored by:	The FreeBSD Foundation
Differential Revision:	https://reviews.freebsd.org/D37975
2.5.43
26 Dec 2022 00:17:42
commit hash: f0ad33c97058797833eb702ce8f3e52a47c9848ccommit hash: f0ad33c97058797833eb702ce8f3e52a47c9848ccommit hash: f0ad33c97058797833eb702ce8f3e52a47c9848ccommit hash: f0ad33c97058797833eb702ce8f3e52a47c9848c files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.5.43

Sponsored by:	The FreeBSD Foundation
2.5.42
01 Oct 2022 20:59:13
commit hash: e2b35d714732ea5fda50b45e26397bb57467ed81commit hash: e2b35d714732ea5fda50b45e26397bb57467ed81commit hash: e2b35d714732ea5fda50b45e26397bb57467ed81commit hash: e2b35d714732ea5fda50b45e26397bb57467ed81 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/hyphy: Not broken on systems where OpenMP isn't available

PR:		265677
Reported by:	Robert Clausecker <fuz@fuz.su>
2.5.42
01 Oct 2022 20:59:13
commit hash: d6b3e9f9c4f0c871c5625927378da900a3d81543commit hash: d6b3e9f9c4f0c871c5625927378da900a3d81543commit hash: d6b3e9f9c4f0c871c5625927378da900a3d81543commit hash: d6b3e9f9c4f0c871c5625927378da900a3d81543 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/hyphy: Add tests; Fix ONLY_FOR_ARCHS order
2.5.42
19 Sep 2022 21:10:39
commit hash: e7ac0267cd808860311aec353c8911ef57dec338commit hash: e7ac0267cd808860311aec353c8911ef57dec338commit hash: e7ac0267cd808860311aec353c8911ef57dec338commit hash: e7ac0267cd808860311aec353c8911ef57dec338 files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.5.42

https://github.com/veg/hyphy/compare/2.5.41...2.5.42

Sponsored by:	The FreeBSD Foundation
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
2.5.41
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.5.41
06 Aug 2022 22:23:11
commit hash: 425afd99186373573e39f006238132ff3797801acommit hash: 425afd99186373573e39f006238132ff3797801acommit hash: 425afd99186373573e39f006238132ff3797801acommit hash: 425afd99186373573e39f006238132ff3797801a files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/hyphy: Update 2.5.40 -> 2.5.41

PR:		265677
Approved by:	jrm@ (maintainer)
2.5.40
04 Aug 2022 16:21:46
commit hash: 36aeef9b99e980990c8b58f44e6de9989b31f4c4commit hash: 36aeef9b99e980990c8b58f44e6de9989b31f4c4commit hash: 36aeef9b99e980990c8b58f44e6de9989b31f4c4commit hash: 36aeef9b99e980990c8b58f44e6de9989b31f4c4 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/hyphy: Correct BROKEN message
2.5.40
04 Aug 2022 07:41:22
commit hash: 6a6938ea1094011e9fd9121b2ed00d005ac4418fcommit hash: 6a6938ea1094011e9fd9121b2ed00d005ac4418fcommit hash: 6a6938ea1094011e9fd9121b2ed00d005ac4418fcommit hash: 6a6938ea1094011e9fd9121b2ed00d005ac4418f files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/hyphy: Broken on systems where OpenMP isn't enabled

Reported by:	fallout
Approved by:	portmgr (blanket)
2.5.40
18 Jul 2022 15:40:25
commit hash: c886234c5ae45cac689113d58b99e3c3fb557653commit hash: c886234c5ae45cac689113d58b99e3c3fb557653commit hash: c886234c5ae45cac689113d58b99e3c3fb557653commit hash: c886234c5ae45cac689113d58b99e3c3fb557653 files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.5.40

https://github.com/veg/hyphy/releases/tag/2.5.40
https://github.com/veg/hyphy/compare/2.5.39...2.5.40

Sponsored by:	The FreeBSD Foundation
2.5.39
27 May 2022 02:38:12
commit hash: f519fe65cafbcf5b76341b8817022baaf52ab092commit hash: f519fe65cafbcf5b76341b8817022baaf52ab092commit hash: f519fe65cafbcf5b76341b8817022baaf52ab092commit hash: f519fe65cafbcf5b76341b8817022baaf52ab092 files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.5.39

https://github.com/veg/hyphy/releases/tag/2.5.39hf1

Sponsored by:	The FreeBSD Foundation
2.5.38
24 Apr 2022 18:24:30
commit hash: e2c4d38d483537ebe27531c71a9359aae6135354commit hash: e2c4d38d483537ebe27531c71a9359aae6135354commit hash: e2c4d38d483537ebe27531c71a9359aae6135354commit hash: e2c4d38d483537ebe27531c71a9359aae6135354 files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.5.38

Upstream changes: https://github.com/veg/hyphy/compare/2.5.36...2.5.38

Sponsored by:	The FreeBSD Foundation
2.5.36
21 Feb 2022 20:13:16
commit hash: 73b83478c14b99126db25691ed42c50a36f9c005commit hash: 73b83478c14b99126db25691ed42c50a36f9c005commit hash: 73b83478c14b99126db25691ed42c50a36f9c005commit hash: 73b83478c14b99126db25691ed42c50a36f9c005 files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Fix build with clang 13.0.0

clang 13 complains about duplicate loop unrolling pragmas for clang and
CGG.  According to [1], clang supports #pragma GCC unroll with identical
semantics to #pragma clang loop unroll, so remove instances of #pragma
clang loop unroll and #pragma unroll when they appear with #pragma GCC
unroll for the same loop.

[1]
https://clang.llvm.org/docs/AttributeReference.html#pragma-unroll-pragma-nounroll

Sponsored by:	The FreeBSD Foundation
2.5.36
03 Feb 2022 05:42:15
commit hash: f557264cccfee6634ab70909733cdb5049b6268bcommit hash: f557264cccfee6634ab70909733cdb5049b6268bcommit hash: f557264cccfee6634ab70909733cdb5049b6268bcommit hash: f557264cccfee6634ab70909733cdb5049b6268b files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.5.36

https://github.com/veg/hyphy/releases/tag/2.5.36

Sponsored by:	The FreeBSD Foundation
2.5.33
17 Nov 2021 11:51:41
commit hash: 913c9fbc40fc1b563ed99af4371fcc05eaec624ccommit hash: 913c9fbc40fc1b563ed99af4371fcc05eaec624ccommit hash: 913c9fbc40fc1b563ed99af4371fcc05eaec624ccommit hash: 913c9fbc40fc1b563ed99af4371fcc05eaec624c files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.5.33

https://github.com/veg/hyphy/releases/tag/2.5.33
2.5.32
12 Nov 2021 14:48:47
commit hash: 40dbbdf79c63cb6b89ffc8e4ecacb61bfd970ececommit hash: 40dbbdf79c63cb6b89ffc8e4ecacb61bfd970ececommit hash: 40dbbdf79c63cb6b89ffc8e4ecacb61bfd970ececommit hash: 40dbbdf79c63cb6b89ffc8e4ecacb61bfd970ece files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/hyphy: enable on armv7
2.5.32
08 Nov 2021 16:49:37
commit hash: 6a7fc8ddc236995f91d6eb7c5d29b7f6b9a601b5commit hash: 6a7fc8ddc236995f91d6eb7c5d29b7f6b9a601b5commit hash: 6a7fc8ddc236995f91d6eb7c5d29b7f6b9a601b5commit hash: 6a7fc8ddc236995f91d6eb7c5d29b7f6b9a601b5 files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/hyphy: enable on powerpc64le
2.5.32
07 Nov 2021 12:14:59
commit hash: 123f5e1c0c00599dd68f3a99e6314202fb702d0fcommit hash: 123f5e1c0c00599dd68f3a99e6314202fb702d0fcommit hash: 123f5e1c0c00599dd68f3a99e6314202fb702d0fcommit hash: 123f5e1c0c00599dd68f3a99e6314202fb702d0f files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/hyphy: enable on powerpc and powerpc64
2.5.32
08 Oct 2021 16:27:33
commit hash: 46ed8da916a0b6ae1eecd597d079adeb2099a5aecommit hash: 46ed8da916a0b6ae1eecd597d079adeb2099a5aecommit hash: 46ed8da916a0b6ae1eecd597d079adeb2099a5aecommit hash: 46ed8da916a0b6ae1eecd597d079adeb2099a5ae files touched by this commit
Mikael Urankar (mikael) search for other commits by this committer
biology/hyphy: Enable on aarch64.
2.5.32
20 Aug 2021 13:56:52
commit hash: dab99da055766eeb61cff4d0064b02b3d0ac69c8commit hash: dab99da055766eeb61cff4d0064b02b3d0ac69c8commit hash: dab99da055766eeb61cff4d0064b02b3d0ac69c8commit hash: dab99da055766eeb61cff4d0064b02b3d0ac69c8 files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.4.32

https://github.com/veg/hyphy/releases/tag/2.5.32

Port changes:
- Remove USES=ssl since it's an indirect dependency from curl
- Remove patch that was upstreamed
2.5.31
05 Jun 2021 23:00:24
commit hash: c33cf04fe57592ec5c03074f022d3bfa917fd2c7commit hash: c33cf04fe57592ec5c03074f022d3bfa917fd2c7commit hash: c33cf04fe57592ec5c03074f022d3bfa917fd2c7commit hash: c33cf04fe57592ec5c03074f022d3bfa917fd2c7 files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.5.31

https://github.com/veg/hyphy/releases/tag/2.5.31
2.5.30
08 Apr 2021 01:54:50
commit hash: ac46e0153758926c19bded89b9418355ac2b3d8acommit hash: ac46e0153758926c19bded89b9418355ac2b3d8acommit hash: ac46e0153758926c19bded89b9418355ac2b3d8acommit hash: ac46e0153758926c19bded89b9418355ac2b3d8a files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/hyphy: Update to 2.5.30
2.5.29
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
2.5.29
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
2.5.29
25 Feb 2021 01:39:51
Revision:566516Original commit files touched by this commit
jrm search for other commits by this committer
biology/hyphy: Update to 2.5.29

https://github.com/veg/hyphy/releases/tag/2.5.29
2.5.28
23 Feb 2021 19:09:02
Revision:566423Original commit files touched by this commit
jrm search for other commits by this committer
biology/hyphy: Update to 2.5.28

https://github.com/veg/hyphy/releases/tag/2.5.28
2.5.27
27 Jan 2021 11:33:53
Revision:563045Original commit files touched by this commit
jrm search for other commits by this committer
biology/hyphy: Update to version 2.5.27

https://github.com/veg/hyphy/releases/tag/2.5.27
2.5.26
15 Jan 2021 20:09:29
Revision:561665Original commit files touched by this commit
jrm search for other commits by this committer
biology/hyphy: Update to version 2.5.26

https://github.com/veg/hyphy/releases/tag/2.5.26
2.5.25_1
11 Jan 2021 17:54:42
Revision:561239Original commit files touched by this commit
jrm search for other commits by this committer
biology/hyphy: Remove USES=compiler:openmp

USES=compiler:openmp still forces building with GCC.  This is no longer
necessary on tier 1 platforms, which have openmp in the base system.

PR:		247753, 252379
2.5.25
11 Jan 2021 02:51:30
Revision:561185Original commit files touched by this commit
jrm search for other commits by this committer
biology/hyphy: Update to version 2.5.25

https://github.com/veg/hyphy/releases/tag/2.5.25
2.5.24
20 Dec 2020 20:21:53
Revision:558773Original commit files touched by this commit
jrm search for other commits by this committer
biology/hyphy: Update to version 2.5.24

https://github.com/veg/hyphy/releases/tag/2.5.24
2.5.23
19 Nov 2020 10:53:56
Revision:555698Original commit files touched by this commit
jrm search for other commits by this committer
biology/hyphy: Update to version 2.5.23

Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.23
2.5.22
18 Nov 2020 10:54:04
Revision:555628Original commit files touched by this commit
jrm search for other commits by this committer
biology/hyphy: Update to version 2.5.22

Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.22hf
2.5.21
30 Oct 2020 14:05:47
Revision:553693Original commit files touched by this commit
jrm search for other commits by this committer
biology/hyphy: Update to version 2.5.21
2.5.20
16 Oct 2020 23:43:17
Revision:552526Original commit files touched by this commit
jrm search for other commits by this committer
biology/hyphy: Update to version 2.5.20
2.5.19
13 Oct 2020 01:05:45
Revision:552165Original commit files touched by this commit
jrm search for other commits by this committer
biology/hyphy: Update to version 2.5.19

Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.19
2.5.18
02 Sep 2020 17:47:10
Revision:547370Original commit files touched by this commit
jrm search for other commits by this committer
biology/hyphy: Update to version 2.5.18 and add AVX option

The AVX option is off by default, because hyphy will crash on systems
without advanced vector extensions support.
2.5.17
20 Aug 2020 16:15:22
Revision:545538Original commit files touched by this commit
jrm search for other commits by this committer
biology/hyphy: Update to version 2.5.17

Upstream changes:
https://github.com/veg/hyphy/releases/tag/2.5.16
https://github.com/veg/hyphy/releases/tag/2.5.17
2.5.15
28 Jun 2020 16:40:34
Revision:540728Original commit files touched by this commit
jrm search for other commits by this committer
biology/hyphy: Update to version 2.5.15

Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.15
2.5.14
30 May 2020 19:39:11
Revision:537106Original commit files touched by this commit
jrm search for other commits by this committer
biology/hyphy: Update to version 2.5.14

Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.14
2.5.12
03 May 2020 02:08:20
Revision:533731Original commit files touched by this commit
jrm search for other commits by this committer
biology/hyphy: Update to version 2.5.12

Upstream changes:

https://github.com/veg/hyphy/releases/tag/2.5.11
https://github.com/veg/hyphy/releases/tag/2.5.12
2.5.10
25 Apr 2020 00:33:17
Revision:532908Original commit files touched by this commit
jrm search for other commits by this committer
biology/hyphy: Update to version 2.5.10

Upstream changes:
https://github.com/veg/hyphy/releases/tag/2.5.9
https://github.com/veg/hyphy/releases/tag/2.5.10
2.5.8
28 Mar 2020 12:27:11
Revision:529331Original commit files touched by this commit
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
2.5.7
20 Mar 2020 01:30:46
Revision:528753Original commit files touched by this commit
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
2.5.6
17 Mar 2020 18:17:16
Revision:528590Original commit files touched by this commit
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
2.5.5
02 Mar 2020 01:31:57
Revision:527606Original commit files touched by this commit
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
2.5.4
21 Feb 2020 12:22:17
Revision:526622Original commit files touched by this commit
jrm search for other commits by this committer
biology/hyphy: Update to version 2.5.4

Upstream changes: https://github.com/veg/hyphy/releases
2.3.14.16_2
26 Jul 2019 20:46:57
Revision:507372Original commit files touched by this commit
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
2.3.14.16_1
25 Dec 2018 20:25:40
Revision:488341Original commit files touched by this commit
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
2.3.14.16_1
12 Dec 2018 01:35:36
Revision:487272Original commit files touched by this commit
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
2.3.14.16
20 Oct 2018 12:21:15
Revision:482495Original commit files touched by this commit
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
2.3.13
22 May 2018 22:55:18
Revision:470664Original commit files touched by this commit
jrm search for other commits by this committer
biology/hyphy: Update to version 2.3.13
2.3.12_1
14 May 2018 16:52:40
Revision:469922Original commit files touched by this commit
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
2.3.12
11 May 2018 00:05:16
Revision:469604Original commit files touched by this commit
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: 68