                     TreeStat v1.2 2005-2008
                    Tree Statistics Generator
                              by
             Andrew Rambaut and Alexei J. Drummond

              Institute of Evolutionary Biology
                    University of Edinburgh
                      a.rambaut@ed.ac.uk

                Department of Computer Science
                     University of Auckland
                    alexei@cs.auckland.ac.nz


UNIX / Mac OS X / Linux / Windows README 
andrew.rambaut@zoo.ox.ac.uk - 29 November 2008

Contents:
1) INTRODUCTION
2) INSTALLING AND RUNNING TRACER
3) PROCESSING TREE FILES
4) VERSION HISTORY
5) SUPPORT & LINKS
6) ACKNOWLEDGMENTS

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1) INTRODUCTION

TreeStat is a program that can calculate a number of statistics or
properties of a set of trees in a tree file. One use of this is to process
trees produced by Bayesian MCMC applications such as BEAST and MrBayes,
calculating statistics which can then be analysed in Tracer.

BEAST - <http://beast.bio.ed.ac.uk/>

MrBayes - <http://morphbank.ebc.uu.se/mrbayes/>

Tracer - <http://beast.bio.ed.ac.uk/Tracer/>

___________________________________________________________________________
2) INSTALLING AND RUNNING TREESTAT

Mac OS X: To install TreeStat, simply drag the program file to where you
normally put applications. Then double click to run.

Windows: To install TreeStat, simply drag the program file to where you
normally put applications. Then double click to run.

Linux / UNIX: Copy or move the folder to where you normally put
applications and then double click the "treestat.jar" file to run or type
"./run_treestat.sh" at the command-line. 

___________________________________________________________________________
3) PROCESSING TREE FILES

Once TreeStat is running, select the statistics you wish to use by
selecting them in the left hand table and pressing the green arrow button.
Selecting a single statistic will provide information about it. Once the
required statistics are selected press the "Process Tree File..." button or
menu option.

You will then be asked to select a tree file to process. This should be in
either PHYLIP or NEXUS format. You will then be asked to provide the name
of the file to which the statistics will be written. 

___________________________________________________________________________
4) VERSION HISTORY

---Version 1.2 29 Nov 2008---

* Add a few new statistics including obtaining attributes written by BEAST
(such as 'rate') at particular MRCAs or averaged over clades.

---Version 1.1 27 June 2007---

* Fixed bugs in the Gamma & Delta statistic
* Add a few new statistics

---Version 1.0 28 Sept 2005---

* First released verson

___________________________________________________________________________
5) SUPPORT & LINKS

Please email us to discuss any problems:

a.rambaut@ed.ac.uk
alexei@cs.auckland.ac.nz

___________________________________________________________________________
6) ACKNOWLEDGMENTS

Thanks to the following for supplying code or assisting with the creation
or testing of BEAST and its associated software:

	Alexander Alekseyenko
	Erik Bloomquist
	Roald Forsberg
	Joseph Heled
	Simon Ho
	Philippe Lemey
	Gerton Lunter
	Sidney Markowitz
	Tulio de Oliveira
	Oliver Pybus
	Beth Shapiro
	Korbinian Strimmer
	Marc Suchard
	+ numerous other users who have kindly helped make BEAST better.
