/usr/share/hyphy/UserAddins/MeanPairwiseDivergence 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 58 59 60 61 62 63 64 65 66 67 68 69 | treeCount = Rows ("Tree");
if (treeCount > 0)
{
treeChoices = {treeCount,2};
for (k=0; k<treeCount; k=k+1)
{
GetString (treeID, Tree, k);
treeChoices [k][0] = treeID;
treeChoices [k][1] = "Tree " + treeID;
}
chosenTree = 0;
if (treeCount > 1)
{
ChoiceList (chosenTree, "Which tree?", 1, SKIP_NONE, treeChoices);
if (chosenTree < 0)
{
return;
}
}
LoadFunctionLibrary("TreeFunctions");
computeMultFactors (treeChoices[chosenTree][0]);
divInfo = computeTotalDivergence (treeChoices[chosenTree][0]);
pInfo = 2*divInfo[0]/leafCount/(leafCount-1);
currentDepth = divInfo[1]/(Abs(treeAVL2)-2);
fprintf (stdout, "Mean pairwise divergence for ",treeChoices[chosenTree][0], " is ", pInfo, "\n");
fprintf (stdout, "Mean branch length for ", treeChoices[chosenTree][0], " is ", currentDepth, "\n");
lf_Count = Rows ("LikelihoodFunction");
if (lf_Count > 0)
{
for (lf_ID = 0; lf_ID < lf_Count; lf_ID = lf_ID + 1)
{
GetString (treeID, LikelihoodFunction,lf_ID);
GetString(lfInfo,^treeID,-1);
lfTrees = lfInfo["Trees"];
for (k = 0; k<Columns(lfTrees); k=k+1)
{
if (lfTrees[k] == treeChoices[chosenTree][0])
{
break;
}
}
if (k < Columns(lfTrees))
{
fprintf (stdout, "\nTree ",Columns(lfTrees)," is a part of likelihood function ", treeID, "\n");
global TreeScalerParameter = 1;
COVARIANCE_PARAMETER = "TreeScalerParameter";
ExecuteCommands ("ClearConstraints("+treeChoices[chosenTree][0]+");ReplicateConstraint (\"this1.?.?:=TreeScalerParameter*this2.?.?__\","+treeChoices[chosenTree][0]+","+treeChoices[chosenTree][0]+");\n");
COVARIANCE_PRECISION = 0.95;
ExecuteCommands ("CovarianceMatrix(cmx,"+treeID+");");
fprintf (stdout, "\nMultiplicative range ", cmx[0], "-", cmx[2], "\n");
fprintf (stdout, "Mean pairwise divergence: ", pInfo, " (", pInfo*cmx[0],",",pInfo*cmx[2],")\n");
fprintf (stdout, "Mean branch length divergence: ", currentDepth, " (", currentDepth*cmx[0],",",currentDepth*cmx[2],")\n");
return {"MEAN PAIRWISE DIVERGENCE": {{pInfo, pInfo*cmx[0], pInfo*cmx[2]}},
"MEAN BRANCH LENGTH": {{currentDepth, currentDepth*cmx[0],currentDepth*cmx[2]}}};
}
}
}
}
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