Geneious KAREN Network Plugin
Welcome to the third release of the new Geneious plugins for grid computing on BeSTGRID.
Biomatters Ltd and The Bioinformatics Institute New Zealand are working together to make available a suite of grid-computing bioinformatics applications for BeSTGRID users, with funding support from REANNZ Ltd and TelstraClear Ltd. All of the applications will work with the free Basic version of Geneious, as well as Geneious Pro.
This third software release includes a range of software specifically tailored to run on BeSTGRID. It also includes a workflow tool that can be used to run a suite of analyses together.
Download Instructions
- Step 1
Download Geneious and install it (the KAREN Network Plugin v.3 requires Geneious 4.5.2 or above). - Step 2
Download and install the KAREN Network Plugin for your operating system:
- Step 3
The KAREN Network Plugin comes bundled with a Command Line Interface Plugin, which allows you to run any program on the grid by writing an XML configuration file. You can generate these config files using the Command Line Interface Creator plugin (see below), or you can make them yourself using these instructions and example files.
For increased functionality, download and install your choice of the following plugins:
Workflow/BLAST Plugin
The Workflow Plugin automates some common bioinformatics tasks. This plugin also includes BLAST
PAUP* (required for workflows)
PAUP* is a popular phylogenetic inference program. Includes Modeltest (GPL).
Clustal (required for workflows)
Clustal is a well know sequence alignment program. This plugin provides graphs of Entropy scores on the generated alignments, so that you can see which parts of the alignment are good and bad.
Command Line Interface Creator
Use the Command Line Interface Creator to generate an XML description of a command line program and its options. This XML file is used by Geneious to develop a dialog box so that a user can run the program within Geneious GUI.
MrBayes
MrBayes is a program for the Bayesian estimation of phylogeny.
LAMARC
LAMARC performs Markov Chain Monte Carlo likelihood estimation population-genetic parameters such as population size, population growth rate, recombination rate, and migration rates.
- Step 4
To access the grid, you will need to set up a security certificate if you have not already done so. The easiest way to do this is using a program called Grix. Please contact your grid adminstrator or one of the Registration Authority Operators for details.
Queries about future versions of the client, and requests for additional features, should be directed to Professor Allen Rodrigo (a.rodrigo@auckland.ac.nz), Director of the Bioinformatics Institute New Zealand and Principal Investigator on the project. For software support, email support@geneious.com.