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| if (Rows (modelMatrixList) == 0) | |
| { | |
| modelMatrixList = | |
| { | |
| {"Equal Input", "EIAA.mdl", "19"} | |
| {"Dayhoff","Dayhoff.mdl","0"} | |
| {"Dayhoff+F","Dayhoff_F.mdl","19"} | |
| {"JTT", "Jones.mdl", "0"} | |
| {"JTT+F", "Jones_F.mdl", "19"} | |
| {"WAG", "WAG.mdl", "0"} | |
| {"WAG+F", "WAG_F.mdl", "19"} | |
| {"rtREV", "rtREV.mdl", "0"} | |
| {"rtREV+F", "rtREV_F.mdl", "19"} | |
| {"mtMAM", "mtMAM.mdl", "0"} | |
| {"mtMAM+F", "mtMAM_F.mdl", "19"} | |
| {"mtREV 24", "mtREV_24.mdl", "0"} | |
| {"mtREV 24+F", "mtREV_24_F.mdl", "19"} | |
| {"HIV within", "HIVwithin.mdl", "0"} | |
| {"HIV within+F", "HIVwithin+F.mdl", "19"} | |
| {"HIV between", "HIVbetween.mdl", "0"} | |
| {"HIV between+F", "HIVbetween+F.mdl", "19"} | |
| {"REV-1 step", "reducedREV.mdl", "19"} | |
| {"REV", "mtREV.mdl", "19"} | |
| }; | |
| } | |
| /*___________________________________________________________________________________________________________*/ | |
| function runAModel (modelID, fileName, xtraP, midx) | |
| { | |
| ExecuteCommands ("#include \"TemplateModels/"+fileName+"\";"); | |
| Tree givenTree = treeString; | |
| LikelihoodFunction lf = (filteredData,givenTree); | |
| GetString (lf_info, lf, -1); | |
| locals = lf_info["Local Independent"]; | |
| if (Columns (branchLengthStash)) | |
| { | |
| USE_LAST_RESULTS = 1; | |
| for (_iv = 0; _iv < Columns (locals); _iv = _iv+1) | |
| { | |
| ExecuteCommands (locals[_iv] + "=1;\n"); | |
| } | |
| currentBL = BranchLength (givenTree,0); | |
| currentBN = BranchName (givenTree,-1); | |
| for (_iv = 0; _iv < Columns (currentBN); _iv = _iv+1) | |
| { | |
| ExecuteCommands ("givenTree."+currentBN[_iv]+".t="+branchLengthStash[_iv]/currentBL+";"); | |
| } | |
| } | |
| else | |
| { | |
| for (_iv = 0; _iv < Columns (locals); _iv = _iv+1) | |
| { | |
| ExecuteCommands (locals[_iv] + "=0.1;\n"); | |
| } | |
| USE_LAST_RESULTS = 1; | |
| } | |
| Optimize (res,lf); | |
| fprintf (stdout, "| ", modelID); | |
| for (k=0; k<maxModelWidth-Abs(modelID)-1; k=k+1) | |
| { | |
| fprintf (stdout, " "); | |
| } | |
| params = res[1][1]+xtraP; | |
| AIC = 2(-res[1][0]+params); | |
| if (filteredData.sites-params>1) | |
| { | |
| cAIC = 2(-res[1][0]+params*(filteredData.sites/(filteredData.sites-params-1))); | |
| } | |
| else | |
| { | |
| cAIC = 0; | |
| } | |
| branchLengths = BranchLength (givenTree,-1); | |
| TL = 0; | |
| for (k=Rows(branchLengths)*Columns(branchLengths)-1; k>=0; k=k-1) | |
| { | |
| TL = TL + branchLengths[k]; | |
| } | |
| fprintf (stdout, "| ", Format (res[1][0],14,3), " | ", Format (params,5,0), " | ", | |
| Format (AIC, 9,3), " | ",); | |
| if (cAIC > 0) | |
| { | |
| fprintf (stdout, Format (cAIC,11,3), " | "); | |
| } | |
| else | |
| { | |
| fprintf (stdout, " N/A | "); | |
| } | |
| fprintf (stdout, Format (TL,11,3), " |\n", sepString); | |
| resultMatrix[midx][0] = res[1][0]; | |
| resultMatrix[midx][1] = params; | |
| resultMatrix[midx][2] = AIC; | |
| resultMatrix[midx][3] = cAIC; | |
| resultMatrix[midx][4] = TL; | |
| if (AIC < bestAIC) | |
| { | |
| bestAIC = AIC; | |
| bestAICidx = midx; | |
| branchLengthStash = BranchLength (givenTree,-1); | |
| } | |
| if (cAIC > 0) | |
| { | |
| if (bestCAIC > cAIC) | |
| { | |
| bestCAIC = cAIC; | |
| bestCAICidx = midx; | |
| } | |
| } | |
| return 0; | |
| } | |
| /*___________________________________________________________________________________________________________*/ | |
| maxModelWidth = 7; | |
| skipCodeSelectionStep = 0; | |
| ChoiceList (doREV, "Include REV?", 1, SKIP_NONE, "Yes", "Include REV and reduced REV models. CAUTION: these models take a long time to fit.", | |
| "No", "Only use empirical models"); | |
| if (doREV < 0) | |
| { | |
| return 0; | |
| } | |
| if (doREV == 0) | |
| { | |
| #include "TemplateModels/chooseGeneticCode.def"; | |
| skipCodeSelectionStep = 1; | |
| } | |
| modelCount = Rows (modelMatrixList) - 2*doREV; | |
| for (k=0; k<modelCount; k=k+1) | |
| { | |
| maxModelWidth = Max(maxModelWidth,Abs (modelMatrixList[k][0])+2); | |
| } | |
| sepString = ""; | |
| capString = ""; | |
| sepString * 256; | |
| sepString * "+"; | |
| capString * 256; | |
| capString * "| Model"; | |
| for (k=0; k<maxModelWidth; k=k+1) | |
| { | |
| sepString * "-"; | |
| } | |
| for (k=0; k<maxModelWidth-6; k=k+1) | |
| { | |
| capString * " "; | |
| } | |
| capString * "| Log Likelihood | #prms | AIC Score | c-AIC Score | Tree Length |\n"; | |
| sepString * "+----------------+-------+-----------+-------------+-------------+\n"; | |
| sepString * 0; | |
| capString * 0; | |
| branchLengthStash = 0; | |
| SKIP_MODEL_PARAMETER_LIST = 0; | |
| #include "TemplateModels/modelParameters2.mdl"; | |
| if (modelType == 1) | |
| { | |
| #include "TemplateModels/defineGamma.mdl"; | |
| } | |
| if (modelType == 2) | |
| { | |
| #include "TemplateModels/defineHM.mdl"; | |
| } | |
| SKIP_MODEL_PARAMETER_LIST = 1; | |
| SetDialogPrompt ("Please load an amino-acid data file:"); | |
| DataSet ds = ReadDataFile (PROMPT_FOR_FILE); | |
| DataSetFilter filteredData = CreateFilter (ds,1); | |
| fprintf (stdout,"\nRunning aminoacid model comparisons on ", LAST_FILE_PATH, "\n\nThe alignment has ",ds.species, " sequences and ", ds.sites, " sites\n"); | |
| _DO_TREE_REBALANCE_ = 1; | |
| #include "queryTree.bf"; | |
| resultMatrix = {modelCount, 5}; | |
| fprintf (stdout, "\n",sepString,capString,sepString); | |
| bestAIC = 1e100; | |
| bestCAIC = 1e100; | |
| bestAICidx = 0; | |
| bestCAICidx = -1; | |
| for (mid=0; mid<modelCount; mid=mid+1) | |
| { | |
| runAModel (modelMatrixList[mid][0], modelMatrixList[mid][1], 0+modelMatrixList[mid][2], mid); | |
| } | |
| fprintf (stdout, "\n\nBest AIC model:\n\t", modelMatrixList[bestAICidx][0], " with the score of ", bestAIC); | |
| if (bestCAICidx>=0) | |
| { | |
| fprintf (stdout, "\n\nBest c-AIC model:\n\t", modelMatrixList[bestCAICidx][0], " with the score of ", bestCAIC); | |
| } | |
| labelMatrix = {{"Log-likelihood","Parameters","AIC","c-AIC","Total tree length",""}}; | |
| aaString = "Model"; | |
| for (fC = 0; fC < modelCount; fC = fC+1) | |
| { | |
| aaString = aaString + ";" + modelMatrixList[fC][0]; | |
| } | |
| USE_LAST_RESULTS = 0; | |
| labelMatrix[5] = aaString; | |
| skipCodeSelectionStep = 0; | |
| OpenWindow (CHARTWINDOW,{{"Model Fits"} | |
| {"labelMatrix"}, | |
| {"resultMatrix"}, | |
| {"Bar Chart"}, | |
| {"Index"}, | |
| {"c-AIC"}, | |
| {"Model Index"}, | |
| {""}, | |
| {"AIC"} | |
| }, | |
| "SCREEN_WIDTH-60;SCREEN_HEIGHT-60;30;30"); |