Read Me

Contents:

1 - What is ModelPie?
2 - Obtaining the program
3 - Installation
	3.a Running from source code
	3.b Running from standalone application
4 - Basic usage
	4.a Setting up
	4.b Running the applications
5 - Future releases
6 - Release history
7 - License
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1 - What is ModelPie?

ModelPie is a natural evolution of MrMTgui (www.genedrift.org/mtgui.php), which is a interface for ModelTest and MrModeltest. ModelPie was created with the ideas of simplifying both the development cycle and the program usage, and increasing its user base by adding MacOSX to the mix.

The original MrMTgui was developed in C++ with wxWidgets as the gui framework. ModelPie is being developed with Python and wxPython, what decreases the code size by almost 1/3, and also makes easier to port the interface to Mac machines. The standalone application size of ModelPie, on the other hand, is larger than release 1.0 of MrMTgui due to the number of Python libraries that need to be included in the package.

2 - Obtaining the program

ModelPie can be found at 

http://www.genedrift.org/modelpie.php
http://code.google.com/p/modelpie
http://sourceforge.net/projects/modelpie/

Both the source code and standalone applications are available in all the above sites.

Source code:

modelpie.py - Linux and Mac Python source
modelpieWIN.py - Windows source

ModelPie.dmg - Mac application
ModelPie.tar.gz - Linux application
ModelPie.exe - Windows installation package

3 - Installation

3.a - Running from source code

ModelPie can be run as a regular Python script. However it needs wxPython to be present in your Python installation. wxPython can be obtained at:

http://www.wxpython.org/download.php

It alos needs two other files, one from ModelTest and the other from MrModelTest: the PAUP blocks to obtain the likelihood scores. Save ModelTest's block as block.dat and MrModelTest's as mrblock.dat in the same directory you have modelpie.py.

To run from source just type in any shell (Windows command prompt, Mac terminal, Linux bash, etc)

> python modelpie.py (on Windows modelpieWIN.py)

3.b - Running from standalone application

- Mac

Open the dmg file, move ModelPie app to your favourite destination and double click it to run. Yep, that easy.

- Linux

Unzip, untar ModelPie.tar.gz and type:

> ./modelpie


- Windows

ModelPie.exe is a installation package. Double click it and follow the instruction. The installer will create a ModelPie item in your Start->Program menu. Select its icon to start ModelPie.


4 - Basic usage

4.a Setting up

ModelPie's interface is almost self explanatory. The window is divided in three basic sections:

on the left, ModelTest's area
on the right, MrModelTest's area and
at the bottom, configuration area

ModelPie cannot be distributed with either PAUP, ModelTest or MrModelTest, so the only option to use these programs is to create a link to them. In the configuration area you have four buttons:

MT path - for ModelTest's path
PAUP path - for Paup's path
MrMT path - for MrModelTest's path and
Check paths - that checks the current links

On your first run, no button in the ModelTest and MrModelTest areas will be enabled. In order to enable them you have to set tha paths to the different applications.

Clicking on the path buttons will open a system dialog. Browse to the location of the executable of the button you clicked on and select it. Repeat for all the programs and you will notice that the buttons will be enabled. To check the results just click on "Check paths" and the executables (and thei locations) will be displayed on the middle of the window).

If everything is fine you are ready to use ModelPie.

4.b Running the applications

ModelPie allows you to run PAUP, ModelTest and MrModelTest.

Starting with PAUP: you can either run PAUP for ModelTest likelihood calculation or for MrModelTest. If you click on the left-hand "Run Paup" button, ModelPie will ask you for a nexus file location and will start running PAUP automatically. Be sure not to have a PAUP block in your file as it might cause problems. If you click on the right-hand "Run Paup" button, the same procedure is taken with the difference of the calculation being based on MrModelTest's PAUP block.

In both cases, ModelPie will display a dialog with a progress bar indicating the current model being analysed. At the end of PAUP run you will be presented with a question: "Do you want to run Mr/ModelTest on your result from PAUP?". If you click YES, ModelPie call Mr/ModelTest and displays the result on the textbox in the middle.

Starting with a scores file: If you already have your scores file you can click on Mr/ModelTest!!! button, select the file on the dialog and see the result in the main textbox. With ModelTest you have the option to use BIC calculation too, and if you choose to use it just check the box.

Saving the scores file: You can also save the scores file generated by PAUP, by clicking on the buttons.


5 - Future versions

If you use MrMtgui you will notice two main differences: less buttons and less functions (still!!) on ModelPie. I am working to include the following:

- automatic nexus file edition
- save the Mr/ModelTest result file
- decrease file size for Mac
- anything that you might want

6 - Release history

Version 1.0 - released on March 15th 2007



The MIT License

Copyright (c) 2007, Paulo Nuin

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.