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+# TransPhylo
+# Introduction #
+
+This is the homepage of TransPhylo, a software package for the Bayesian inference of infectious disease transmission from a phylogeny. The input is a dated phylogeny, where leaves correspond to pathogens isolated from the infected hosts. The main output is a transmission tree which indicates who infected whom. Such reconstruction can be achieved by colouring the branches of the phylogeny using a separate colour for each host, and such that the subtree coloured in a given colour represents the evolution happening within the corresponding host. Changes of colours on branches therefore correspond to transmission events from one host to another.
+
+A more formal description of the statistical methodology underpinning TransPhylo has been published in 2014 in the scientific journal Molecular Biology and Evolution. This article is entitled [Bayesian inference of infectious disease transmission from whole genome sequence data](http://biorxiv.org/content/early/2013/12/16/001388) and was authored by [Xavier Didelot](http://www.xavierdidelot.xtreemhost.com/)  from Imperial College London, [Jennifer Gardy](http://jennifergardy.com/) from the University of British Columbia and [Caroline Colijn](http://www.imperial.ac.uk/AP/faces/pages/read/Home.jsp?person=c.colijn) from Imperial College London.
+
+# Download #
+
+You can download the [Matlab](http://www.mathworks.co.uk/products/matlab/) source code for TransPhylo via GIT using the command:
+```
+git clone https://github.com/xavierdidelot/TransPhylo.git
+```
+
+You will need [Matlab](http://www.mathworks.co.uk/products/matlab/) to use this code. The [bioinformatics toolbox](http://www.mathworks.co.uk/products/bioinfo/) is not strictly required but used for some of the graphical outputs.
+
+Please note that the code for TransPhylo is distributed under the terms of the GNU GPL v3 license, for more details see https://www.gnu.org/copyleft/gpl.html
+
+To generate a timed phylogeny which is the input required by TransPhylo, you may want to use [BEAST](http://beast.bio.ed.ac.uk/) or [BEAST2](http://www.beast2.org/wiki/index.php/Main_Page).
+
+# Tutorial #
+
+If you are new to TransPhylo, you can follow this [tutorial](https://github.com/xavierdidelot/TransPhylo/wiki/Tutorial) which should only take a few minutes to go through and describes the main functionalities of TransPhylo, including simulating datasets, inferring the transmission tree given a phylogeny and several graphical representations.
+
+# Getting help #
+
+If you need assistance using TransPhylo, you can get in touch by emailing `[email protected]`