MPP - Microarray-To-Phylogeny Pipeline
Colney Lane, Norwich, NR4 7UH, UK.
Telephone: +44(0) 1603 450597 (direct)
+44(0) 1603 450000 (switchboard)
Fax: +44(0)1603 450595
Downloads and Help Pages
Last MPP Update = 28.12.06
Version 2 of MPP is now available! Please find the new source code and executable downloads below.
MPP help
Link to the most recent help files and javadocs for MPP online.
MPP Prerequisites
Microarray analysis
MPP relies on some existing software, and installation notes are included as part of the MPP help files. These files are included in the MPP distribution and source code downloads, the .tarballs containing *nix packages, the zips containing Windows packages. Here is a list of links to the relevant software that MPP needs preinstalled for it to function properly:
- Java Runtime Environment 5. MPP cannot be compiled and cannot be run under 1.4.2 - Java 5 is essential!
- R- Statistical computation and graphics software
- Biobase - BioConductor utility R package
- vsn - BioConductor R package for variance stabilisation
- MCLUST - R package for model-based clustering
- Rserve - TCP-based R connector software
We suggest using the SplitsTree package to construct and draw trees and networks. SplitsTree 4, also known as JSplits, is a Java implementation of the previous SplitsTree incarnations, which is available as a beta version here.
You can also read about the required software for MPP in the help pages.
MPP downloads
The latest MPP release version is 2.0. There is work pending on this release, but the main functionality of MPP is available.
The tarballs are for *nix systems, and the .zip are for Windows but they contain the same files. Version 1.0 is now no longer available.
Installation instructions can be found in the online help, or in the local version packaged with MPP.
The full MPP distribution files, containing the MPP jar binary executable, source code, the help files, javadocs and required libraries.
| File Name | File Size |
|---|---|
| mpp-2.0.zip | 8.9MB |
| mpp-2.0.tar.gz | 8.6MB |
The full MPP source code, including the relevant build scripts and dependencies for Windows and *nix.
| File Name | File Size |
|---|---|
| mpp-2.0-src.zip | 8.9MB |
| mpp-2.0-src.tar.gz | 8.5MB |
The most recent javadocs only.
| File Name | File Size |
|---|---|
| mpp-2.0-javadoc.zip | 525KB |
| mpp-2.0-javadoc.tar.gz | 230KB |
Third-party plugins
There are no third-party plugin modules available for MPP as yet.
Publications relating to MPP
- Davey RP, Savva G, Dicks J and Roberts IN (2007) MPP: A Microarray-To-Phylogeny Pipeline for Analysis of Gene and Marker Content Datasets. Bioinformatics 23 (8): 1023-1025 Link to copy in PDF format
- Davey R (2005) Refinement and Validation of Algorithms for Deduction of Gene Content from CGH Microarrays. PhD dissertation
- Davey R, Lacey G, MacKenzie DA, Defernez M, Mellon F, Huber K, Moulton V and Roberts IN (2005) Comparative metabolomics of Saccharomyces yeasts. First FEBS Advanced Course on Systems Biology: From Molecules & Modeling To Cells March 12- 18, 2005, Gosau, Austria, EU
- Davey RP, Roberts IN, Dicks JL and Rayward-Smith VJ (2004) MPP: A microarray-to-phylogeny pipeline for gene content analysis. ISMB/ECCB 2004, July 31 - August 4, 2004, Glasgow, UK
Designed and maintained by Virginia Barnard
LAST UPDATED: 21st September 2005
