PhyTB: Phylogeny and sample positioning for Tuberculosis v.2.0 18/3/2015

• homepage: http://pathogenseq.lshtm.ac.uk/phytblive/index.php
• source code: https://sourceforge.net/projects/phylotrack/

Overview

PhyloTrack is a JavaScript-based library for the interactive study of variation in clonal microorganisms, where the genomes of several isolates after been sequenced and their data analysed will be incorporated into an application with high user interactive functionality. The tools for the transformation of the data are written in Perl and Python. The resulting application consists of a Phylogenetic tree, a Map view, a Genome Browser and a processing tool for the Positioning of Samples in the phylogenetic tree.

Quick Start

On Linux/OSX, in order to use the data-transformation scripts to create your own datasets to feed into the PhyTB tool you will need to download all the perl/python (.pl/.py) scripts from the source code site:

• Source code: https://sourceforge.net/projects/phylotrack/files/

To deploy the actual PhyTB tool "as it is" with the default data you will need to download the latest version of the tool (PhyTB.vX.zip):

• Source code: https://sourceforge.net/projects/phylotrack/files/

Dependencies

For running the Phylotrack scripts you will need to have installed:

• Python 2.7.x: https://python.org/
• Python tkinter module: https://docs.python.org/2/library/tkinter.html

In order to install the PhyTB tool you will need to have installed on your machine:

• A server of your choice (PhyTB was deployed under apache2)

http://httpd.apache.org/

On linux:

sudo apt-get install apache2

• A PHP extension installed in your server(PhyTB was deployed using PHP5).

http://php.net/

On linux:

sudo apt-get install php5 libapache2-mod-php5

Remember to restart your apache server after installation:

sudo /etc/init.d/apache2 restart

• An instance of tabix compiled version (copied from the "/bin" folder inside tabix) in your server.

http://samtools.sourceforge.net/tabix.shtml

On linux:

sudo apt-get install tabix

The version of JBrowse used in this tool is the version 1.11.5 (the latest available at the time of implementation) in order to install your own verion follow the link http://jbrowse.org/code/JBrowse-1.10.2/docs/tutorial/.

Running

To have your own copy of PhyTB runnning uncompress the zip file in the root folder of your server:

unzip PhyTB.vx.zip ./

And make sure that the folder "files" inside PhyTB root folder has read-write access from all the users.

chmod 766 ./files

Input File

The only need (if everything has been installed correctly) for the server to be able to perform a sample positioning is a non-compressed VCF file (extension .vcf).

An example of file input is presented here:

http://pathogenseq.lshtm.ac.uk/phytblive/ERR229993.filt.vcf

Documentation

See: https://sourceforge.net/p/phylotrack/wiki/Home/

Author

Please contact Ernest Diez Benavente (ediezben@gmail.com), if you have any questions/issues.