/usr/share/hyphy/UserAddins/BranchLengthCI 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 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 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 | RequireVersion ("0.9920060424");
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;
}
}
chosenTree = treeChoices[chosenTree][0];
mxTreeSpec = {5,1};
mxTreeSpec [0] = chosenTree;
mxTreeSpec [1] = "8240";
mxTreeSpec [2] = "10,50,-10,-300,1";
mxTreeSpec [3] = "EXPECTED_NUMBER_OF_SUBSTITUTIONS";
mxTreeSpec [4] = "";
OpenWindow (TREEWINDOW, mxTreeSpec);
ExecuteCommands ("nodeNames = BranchName(`chosenTree`,-1)");
nodeCount = Columns (nodeNames)-1;
choiceMatrix = {nodeCount,2};
for (bc=0; bc<nodeCount; bc=bc+1)
{
choiceMatrix[bc][0] = nodeNames [bc];
choiceMatrix[bc][1] = choiceMatrix[bc][0];
}
ChoiceList (stOption,"Choose branches to test",1,NO_SKIP,choiceMatrix);
if (stOption < 0)
{
return -1;
}
chosenBranch = choiceMatrix[stOption][0];
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);
ExecuteCommands ("GetString(lfInfo,`treeID`,-1);");
lfTrees = lfInfo["Trees"];
for (k = 0; k<Columns(lfTrees); k=k+1)
{
if (lfTrees[k] == chosenTree)
{
break;
}
}
if (k < Columns(lfTrees))
{
fprintf (stdout, "\nTree ",Columns(lfTrees)," is a part of likelihood function ", treeID, "\n");
global TreeScalerParameter = 1;
ExecuteCommands ("ClearConstraints(`chosenTree`);");
cte = "ReplicateConstraint (\"this1.`chosenBranch`.?:=TreeScalerParameter*this2.`chosenBranch`.?__\",`chosenTree`,`chosenTree`);";
ExecuteCommands(cte);
COVARIANCE_PRECISION = 0.95;
COVARIANCE_PARAMETER = "TreeScalerParameter";
ExecuteCommands ("CovarianceMatrix(cmx,"+treeID+");");
fprintf (stdout, "\nMultiplicative range ", cmx[0], "-", cmx[2], "\n");
ExecuteCommands ("bl = BranchLength (`chosenTree`,stOption)");
fprintf (stdout, "\n", chosenBranch, " has a branch length of ", bl, " (", bl*cmx[0],",",bl*cmx[2],")\n");
}
}
}
}
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