/usr/share/hyphy/TemplateBatchFiles/AnalyzeNucDataFreq2.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 47 48 49 50 51 52 53 54 55 56 57 | SetDialogPrompt ("Please specify a nuleotide data or aminoacid file:");
DataSet ds = ReadDataFile (PROMPT_FOR_FILE);
DataSetFilter filteredData = CreateFilter (ds,1);
global estPiA = 0.25;
global estPiC = 0.25;
global estPiG = 0.25;
global estPiT = 0.25;
global sum;
estPiA:<1;
estPiC:<1;
estPiG:<1;
estPiT:=Abs(1-estPiA-estPiC-estPiG);
sum := estPiA+estPiC+estPiG+estPiT;
global estPiAR = 0.25;
global estPiCR = 0.25;
global estPiGR = 0.25;
global estPiTR = 0.25;
global sumR;
estPiAR:<1;
estPiCR:<1;
estPiGR:<1;
estPiTR:=Abs(1-estPiAR-estPiCR-estPiGR);
sumR := estPiAR+estPiCR+estPiGR+estPiTR;
EMBED_FREQUENCY_DEPENDENCE = 1;
SelectTemplateModel(filteredData);
estPiA = .25;
estPiC = .25;
estPiG = .25;
vectorOfFrequencies = {{estPiA/sum},{estPiC/sum},{estPiG/sum},{estPiT/sum}};
vectorOfFrequenciesRoot = {{estPiAR/sumR},{estPiCR/sumR},{estPiGR/sumR},{estPiTR/sumR}};
fprintf (stdout,"\n",ds);
_DO_TREE_REBALANCE_ = 0;
ACCEPT_ROOTED_TREES = 1;
#include "queryTree.bf";
LikelihoodFunction3 lf = (filteredData,givenTree,vectorOfFrequenciesRoot);
Optimize (res,lf);
fprintf (stdout, "\n",lf);
HarvestFrequencies (obsFreq,filteredData,1,1,1);
fprintf (stdout, "\nEstimated Root Frequencies:\n", vectorOfFrequenciesRoot,
"\nEstimated Matrix Frequencies:\n", vectorOfFrequencies,
"\nObserved Frequencies\n", obsFreq);
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