Getting Started with vPhyloMM
(Bacheler Dataset)

1. Make sure to have installed vPhyloMM and its dependencies (see Installation/).
2. It is highly recommended to read the perldoc that comes with vPhyloMM at:
perldoc Run_vPhyloMM.pl
perldoc vPhyloMM.pm
perldoc vPhyloMM_GUI.pm

3. To create a new variables file containing the default settings use:
perl Run_vPhyloMM.pl --new=<FILENAME>
4. To immediately run vPhyloMM from the command line, terminal, or shell use:
perl Run_vPhyloMM.pl --variables-file=sample_variables.txt
This is equivalent to immediately clicking "go" in the GUI (described below) but does not load any of the GUI dependencies. It is acceptable for calling vPhyloMM from a script or remote terminal. This might be your only option if you are unable or do not wish to install ActivePerl because of a known bug with the perl.org distribution of perl and the Tkx module.
5. An interactive GUI is also available if the --gui flag is used:
perl Run_vPhyloMM.pl --variables-file=sample_variables.txt --gui
6. Once the vPhyloMM window has loaded, it will be ready to run the vPhyloMM algorithm on the sample “Bacheler dataset” which is freely available at http://sourceforge.net/projects/vphylomm/files/bacheler_dataset.tar.gz/download. It should be unzipped into the same directory as vPhyloMM, placing a folder named 'DNA' and a markers file named 'markers.txt' there.
7. Select which reports will be generated in the “program_options” section.
8. The executable for Sliding MinPD is called minpd or minpd.exe on Windows machines (Important! See Installation/Sliding MinPD.pdf for instructions on setting up minpd properly). If the Sliding MinPD executable is not in your system path (typing minpd at the command prompt does not run Sliding MinPD) then you will need to tell vPhyloMM where to find it by setting the SlidingMinPD variable.
   • Click on the “+” symbol to the left of "SlidingMinPD".
   • Type the path or click the box labled “...” and browsing there (see image below). This will be the same directory that you chose in step 5 of Sliding MinPD installation.
   • 
9. The same applies for the R executable, although the default setting here should work if R has been properly installed (see 2_R.pdf).
10. Choose the main output directory. This can be an absolute or relative path and is the directory where the results will be stored. If it does not exist, vPhylomm will create it if possible. The default is "Bachelor Dataset".
11. The settings are reset each time vPhylomm is loaded. To save your settings:
    • Click on "File->Save As..."
    • In the upper left-hand corner of the window. Choose a folder and a name for the setting and click Save.
12. To recall your settings:
    • Clicking on "File->Open..." and choose your saved file.
13. Changes to vPhyloMM settings can also be effected by manually editing the variables file.
14. Optionally, vPhyloMM can graphically map the transitions observed. This option is only available if GraphViz and the GraphViz perl module have been installed.
    To enable graph drawing:
    • In the GUI, check the pathway graphs and pruned pathway graphs boxes under program options.
    • From the CLI, open the variables file and change the value of pathway graphs and pruned pathway graphs to ' 0 '.
15. Click the go button at the bottom to generate the selected reports.
16. The output files will be placed in the "Bacheler Dataset" directory unless you have changed the main output directory.