/usr/share/hyphy/TemplateBatchFiles/AnalyzeDiNucData.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 | SetDialogPrompt ("Please specify a di-nucleotide (e.g. stem RNA) file:");
DataSet ds = ReadDataFile (PROMPT_FOR_FILE);
DataSetFilter filteredData = CreateFilter (ds,2);
fprintf (stdout,"\n______________READ THE FOLLOWING DATA______________\n",ds);
SelectTemplateModel(filteredData);
_DO_TREE_REBALANCE_ = 1;
#include "queryTree.bf";
LikelihoodFunction lf = (filteredData,givenTree);
timer = Time(0);
USE_ADAPTIVE_VARIABLE_STEP = 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);
#include "categoryEcho.bf";
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