Permalink
Fetching contributors…
Cannot retrieve contributors at this time
| NICETY_LEVEL = 3; | |
| #include "TemplateModels/chooseGeneticCode.def"; | |
| #include "simpleBootstrap.bf"; | |
| SetDialogPrompt ("Please specify a codon data file:"); | |
| COUNT_GAPS_IN_FREQUENCIES = 0; | |
| VERBOSITY_LEVEL = 1; | |
| DataSet ds = ReadDataFile (PROMPT_FOR_FILE); | |
| DataSetFilter filteredData = CreateFilter (ds,3,"","",GeneticCodeExclusions); | |
| fprintf (stdout,"\n______________READ THE FOLLOWING DATA______________\n",ds); | |
| SelectTemplateModel(filteredData); | |
| _DO_TREE_REBALANCE_ = 1; | |
| #include "queryTree.bf"; | |
| if (modelType) | |
| { | |
| ChoiceList (branchLengths, "Branch Lengths", 1, SKIP_NONE, | |
| "Estimate", "Estimate branch lengths by ML", | |
| "Proportional to input tree", "Branch lengths are proportional to those in input tree"); | |
| if (branchLengths < 0) | |
| { | |
| return; | |
| } | |
| if (branchLengths == 1) | |
| { | |
| global treeScaler = 1; | |
| ReplicateConstraint ("this1.?.?:=treeScaler*this2.?.?__", givenTree, givenTree); | |
| } | |
| } | |
| LikelihoodFunction lf = (filteredData,givenTree); | |
| Optimize (res,lf); | |
| fprintf (stdout, "\n______________RESULTS______________\n",lf); | |
| /* compute syn and non-syn stencils for current genetic code */ | |
| #include "categoryEcho.bf"; | |
| GetString (sendMeBack,lf,-1); | |
| sendMeBack["LogL"] = res[1][0]; | |
| sendMeBack["NP"] = res[1][1]; | |
| return sendMeBack; |