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