/usr/share/hyphy/TemplateBatchFiles/AnalyzeNucDataFreq.bf is in hyphy-common 2.2.7+dfsg-1.
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 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 | SetDialogPrompt ("Please specify a nuleotide data or aminoacid file:");
DataSet ds = ReadDataFile (PROMPT_FOR_FILE);
DataSetFilter filteredData = CreateFilter (ds,1);
global estPiA;
global estPiC;
global estPiG;
global estPiT;
global sum;
estPiA:<1;
estPiC:<1;
estPiG:<1;
estPiT:=Abs(1-estPiA-estPiC-estPiG);
sum := estPiA+estPiC+estPiG+estPiT;
EMBED_FREQUENCY_DEPENDENCE = 1;
SelectTemplateModel(filteredData);
estPiA = .25;
estPiC = .25;
estPiG = .25;
vectorOfFrequencies = {{estPiA/sum},{estPiC/sum},{estPiG/sum},{estPiT/sum}};
fprintf (stdout,"\n",ds);
_DO_TREE_REBALANCE_ = 1;
#include "queryTree.bf";
LikelihoodFunction lf = (filteredData,givenTree);
Optimize (res,lf);
fprintf (stdout, "\n",lf);
HarvestFrequencies (obsFreq,filteredData,1,1,1);
fprintf (stdout, "\nEstimated Frequencies:", vectorOfFrequencies, "\nObserved Frequencies", obsFreq);
GetString (mbl, TrNModel,-1);
fprintf (stdout,"\n",mbl,"\n");
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