PhyloD -help
PhyloD [many parameters]

Required Arguments:

Optional Arguments:

  • -KeepTest keepTest, default, AlwaysKeep
  • -skipRowIndexFile, a file that tells which output rows to skip because they have already been run, e.g. a file containing "100-200,300-400")
    • As described below, Tabulate.exe audits the output of PhyloD.exe and reports which rows were found. Use this parameter to have PhyloD.exe run again and produce the missing output rows.
  • -optimizer BrentThenGrid (default) OR BrentWithNoGrid OR Grid
    • You can append a tolerance to the Bren methods: e.g. BrentThenGrid.001.
    • The default Brent tolerance is .001.

Output File

Here is an example of an output file's name:

In general, the output file's name is

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

It also contains columns
  • rowIndex, the number of each output row starting with "0"
  • rowCount, the total number of unique rows in the output.
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.

Last edited Apr 19, 2007 at 7:14 PM by CarlK, version 17


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