PhyloD.exe

Usage:

PhyloD -help
PhyloD [many parameters]

Required Arguments:

Optional Arguments:


Output File

Here is an example of an output file's name:
test03062007.DiscreteConditionalEscape.PredictorPermutation.-1-9.1.0.txt

In general, the output file's name is
niceName.leafDistribution.nullDataGenerator.nullIndexRange.pieceCount.pieceIndexRange.txt

It is a tab-delimited text file with a NullIndex column and a PValue column.

It also contains columns The values in these two columns allow Tabulate.exe to audit PhyloD.exe's output. Tabulate.exe ignores duplicate rows and will report on which rows were found.


Example output file

Notes on the Code

The source code almost includes support for joint (as contrasted with conditional) models. To support joint distribution models, you would need to replace the stub files LinearAlgebra\Eigen.cs, LinearAlgebra\ComplexArray.cs, and LinearAlgebra\DoubleArray.cs with code that can find the inverse and Eigenvalues of matricies.