goeBURST

global optimal eBURST

Description

goeBURST is a java implementation of the eBURST algorithm rules proposed by Feil et al, using a graphic matroid approach that ensures an optimal solution for the placement of links between Sequence Types. This implementation uses prefuse a visualization framework for the Java programming language. A Short Tutorial for the software can be found here.

Software

News

Phyloviz software is now avaliable in a beta version!
It uses the goeBURST algorithm, and has all the goeBURST functionalities plus it allows data integration and visualization from other sources.
Download a beta version from here!

goeBURST 1.2.1 version available!
What's new: User can now create groups DLV level (2 differences allowed in the allelic profile) or TLV level (3 differences allowed in the allelic profile). New binaries available for the major operating systems.

This software requires JAVA 1.5 or a more recent version. You can get it here
You can download the jar file (v1.2.1):

This file includes all dependencies, namely the Prefuse visualization toolkit and the VectorGraphics package of the FreeHEP Java library. The dependencies are subject to their own licenses, you should refer to their on-line documentation.

Download binaries

Linux Mac Os X Windows

Datasets

The dataset format needed is flat text file where each line should have 8 tab separated values.The first value is the Sequence Type number and the following 7 values are the allele numbers for each gene. Example from Campylobacter jejuni dataset:

9	1	6	22	24	12	7	1
45	4	7	10	4	1	7	1
11	48	7	10	4	1	7	1
433	2	59	4	38	17	12	35
21	2	1	1	3	2	1	5
14	9	2	55	62	4	5	6
15	6	4	13	2	2	1	5

The datasets used in the publication are provided here for future reference.

Publications

Francisco AP, Bugalho M, Ramirez M, Carrico JA., Global Optimal eBURST analysis of Multilocus typing data using a graphic matroid approach,BMC Bioinformatics 2009, 10:152doi:10.1186/1471-2105-10-152 Abstract

Acknowledgements

Miguel Bugalho was partially supported by Fundação para a Ciência e a Tecnologia (SFRH/BD/13215/2003). This work was partially funded by Fundação para a Ciência e a Tecnologia (PTDC/SAU-ESA/71499/2006). This publication made use of data available at Imperial College MLST.net, University of Oxford PubMLST and Institute Pasteur MLST Databases. We also acknowledge Ed Feil, David Aanansen and Brian Spratt for the eBURST source code and insightful discussions, and Rob Willems for help in the E. faecium analysis and providing the E. faecium data set.