| /dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/models/protein/matrices/ |
| H A D | JTT.ibf | 1 /********* JTT MODEL OF PROTEIN EVOLUTION ************/
12 * @name models.protein.JTT.ModelDescription
17 function models.protein.JTT.ModelDescription(type) {
19 …models.protein.JTT.ModelDescription.model_definition [terms.model.empirical_rates] = models.protei…
20 …models.protein.JTT.ModelDescription.model_definition [terms.model.frequency_estimator] = "models.p…
21 return models.protein.JTT.ModelDescription.model_definition;
51 models.protein.JTT.Rij = {
236 * @name models.protein.JTT.frequencies
237 * @param {Dictionary} Baseline JTT model
238 * @returns {Dictionary} Updated JTT model with empirical frequencies
[all …]
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| /dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/ProteinAnalyses/ |
| H A D | plusF_helper.ibf | 4 "JTT": "models.protein.JTT.ModelDescription",
9 "JTT": models.protein.empirical.JTT.empirical_R,
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| /dports/biology/py-ete3/ete3-3.1.2/ete3/tools/ |
| H A D | ete_build.cfg | 276 _models = "JTT", "WAG", "VT", "LG", "MtREV"
312 _aa_models = "JTT,WAG,VT,LG,MtREV"
320 _desc = 'Test JTT,WAG,VT,LG,MtREV models using NJ tree inference'
322 _aa_models = "JTT,WAG,VT,LG,MtREV"
327 _desc = 'Test JTT,WAG,VT,LG,MtREV models using ML tree inference'
329 _aa_models = "JTT,WAG,VT,LG,MtREV"
334 _desc = 'BioNJ tree inferred with Phyml. default models JTT/GTR'
336 _aa_model = JTT # AA model used if no model selection is performed
363 _aa_model = JTT # AA model used if no model selection is performed
387 _aa_model = JTT # Model used if no model selection is performed
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| /dports/science/openbabel/openbabel-3.1.1/test/pdb_ligands_sdf/ |
| H A D | 4jtt_jtt.sdf | 3 Coordinates from PDB:4JTT:A:409 Model:1 without hydrogens
92 JTT
95 4JTT
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| /dports/biology/mothur/mothur-1.46.1/source/calculators/ |
| H A D | jtt.hpp | 129 class JTT : public DistCalc { class
133 JTT(double c) : DistCalc(c) { name = "JTT (Jones-Taylor-Thornton matrix)"; } in JTT() function in JTT
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| /dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/models/protein/ |
| H A D | empirical.bf | 44 LoadFunctionLibrary("matrices/JTT.ibf");
260 "JTT": "models.protein.JTT.ModelDescription",
271 "JTT": "models.protein.JTTF.ModelDescription",
281 "JTT": "models.protein.JTTML.ModelDescription",
333 /**************************************** JTT functions *************************************/
337 * @name models.protein.JTT.ModelDescription
338 * @description Create the baseline schema (dictionary) for the JTT model of protein evolution
342 function models.protein.JTT.ModelDescription(type) {
344 …models.protein.JTT.ModelDescription.model_definition [terms.model.empirical_rates] = models.protei…
345 …models.protein.JTT.ModelDescription.model_definition [terms.model.frequency_estimator] = "models.p…
[all …]
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| H A D | matrix2dict_aux.bf | 74 JTT = {
97 //fprintf (stdout, mapMatrixToDict (models.protein.alphabet, JTT), "\n"):
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| /dports/biology/p5-BioPerl/BioPerl-1.7.7/t/Tools/Phylo/ |
| H A D | Molphy.t | 21 is($r->model, 'JTT');
31 is($r->model, 'JTT');
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| /dports/biology/p5-BioPerl/BioPerl-1.7.7/t/data/ |
| H A D | lysozyme6.simple.protml | 1 5 / 50 JTT model approx ln L -1047.8 ... -1056.8 diff 9.0
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| H A D | lysozyme6.protml | 113 5 / 50 JTT model approx ln L -1047.8 ... -1056.8 diff 9.0
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| /dports/math/scalapack/scalapack-2.1.0/SRC/ |
| H A D | pstrsen.f | 356 $ IPW1, ITER, ITT, JLOC1, JTT, K, LIWMIN, LLDT, local
508 $ MYROW, MYCOL, ITT, JTT, TRSRC, TCSRC )
510 ELEM = T( (JTT-1)*LLDT + ITT )
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| H A D | pdtrsen.f | 356 $ IPW1, ITER, ITT, JLOC1, JTT, K, LIWMIN, LLDT, local
508 $ MYROW, MYCOL, ITT, JTT, TRSRC, TCSRC )
510 ELEM = T( (JTT-1)*LLDT + ITT )
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| /dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/ |
| H A D | AddABias.ibf | 178 "JTT","JTT",
210 DIRECTORY_SEPARATOR + "JTT";
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| H A D | AAModelComparison.bf | 8 {"JTT", "Jones.mdl", "0"}
9 {"JTT+F", "Jones_F.mdl", "19"}
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| /dports/biology/molden/molden5.8/plush/ |
| H A D | JTT | 1 mol="JTT" Charge="0"
|
| /dports/science/py-DendroPy/DendroPy-4.4.0/src/dendropy/interop/ |
| H A D | seqgen.py | 63 JTT = SubstitutionModel("JTT") variable in SeqGen
70 MODELS = [F84, HKY, GTR, JTT, WAG, PAM, BLOSUM, MTREV, CPREV, GENERAL]
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| /dports/www/chromium-legacy/chromium-88.0.4324.182/net/data/verify_certificate_chain_unittest/intermediate-lacks-basic-constraints/keys/ |
| H A D | Intermediate.key | 24 JTT+FXN0I52dRWTX1M8fJlPh4M0gNC1oG4Bv3gheZOatOVsHcTMhHKtKmcOZVtmU
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| /dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/phylip/src/ |
| H A D | protdist.h | 24 static QString JTT;
|
| /dports/biology/hyphy/hyphy-2.5.33/tests/hbltests/libv3/ |
| H A D | FADE.wbf | 4 …ionAnalyses/FADE.bf", {"--alignment" : PATH_TO_CURRENT_BF + "data/CD2_AA.fna", "--model" : "JTT"});
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| /dports/biology/paml/paml4.9j/dat/ |
| H A D | jones-dcmut.dat | 29 JTT rate matrix prepared using the DCMut method*
|
| /dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/TemplateModels/EmpiricalAA/ |
| H A D | modellist.ibf | 15 /* JTT */
17 (modelList [index])["Name"] = "JTT (Jones,Taylor,Thornton)";
21 (modelList [index])["File"] = "JTT";
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| /dports/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/t/ |
| H A D | Molphy.t | 57 is($r->model, 'JTT');
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| /dports/biology/treepuzzle/tree-puzzle-5.2/ |
| H A D | README | 17 nucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62, VT, WAG for amino acids,
|
| /dports/biology/mafft/mafft-7.267-without-extensions/core/ |
| H A D | mafft-profile.c | 62 TMorJTT = JTT; in arguments()
148 TMorJTT = JTT; in arguments()
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| /dports/biology/mothur/mothur-1.46.1/source/commands/ |
| H A D | distancecommand.cpp | 357 …if (params->calc == "jtt") { distCalculator = new JTT(params->cutoff); … in driverColumn()
430 …if (params->calc == "jtt") { distCalculator = new JTT(params->cutoff); … in driverLt()
509 …if (params->calc == "jtt") { distCalculator = new JTT(params->cutoff); … in driverSquare()
589 …if (params->calc == "jtt") { distCalculator = new JTT(params->cutoff); … in driverFitCalc()
|