From decf2352d36593f28c9d5e61c89f3f79b883cf6e Mon Sep 17 00:00:00 2001 From: Xavier Didelot Date: Thu, 11 Jun 2015 17:07:41 +0100 Subject: [PATCH] Create README.md --- README.md | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 README.md diff --git a/README.md b/README.md new file mode 100644 index 0000000..ec17090 --- /dev/null +++ b/README.md @@ -0,0 +1,27 @@ +# 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 `xavier.didelot@gmail.com`