/usr/share/hyphy/TemplateBatchFiles/AnalyzeNucProtData.bf is in hyphy-common 2.2.6+dfsg-3build3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 | _Genetic_Code = 0;
ExecuteAFile("simpleBootstrap.bf");
SetDialogPrompt ("Please specify a nucleotide or amino-acid data file:");
DataSet ds = ReadDataFile (PROMPT_FOR_FILE);
DataSetFilter filteredData = CreateFilter (ds,1);
fprintf (stdout,"\n______________READ THE FOLLOWING DATA______________\n",ds);
SelectTemplateModel(filteredData);
_DO_TREE_REBALANCE_ = 1;
ExecuteAFile ("queryTree.bf");
LikelihoodFunction lf = (filteredData,givenTree);
timer = Time(0);
Optimize (res,lf);
timer = Time(0)-timer;
fprintf (stdout, "\n______________RESULTS______________\nTime taken = ", timer, " seconds\nAIC Score = ",
2(res[1][1]-res[1][0]),"\n",lf);
ExecuteAFile ("categoryEcho.bf");
GetString (lfInfo, lf, -1);
return {"Log(L)": res[1][0], "DF": res[1][1], "Tree": Format (givenTree,1,1)}
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