Atmosphere Image for using accessory applications with BEAST-2.1.3

This image is intended for creating input files to use in BEAST (using the BEAUti software) or for visualizing and assessing the results of a BEAST analysis. Although you can run BEAST itself in this image, it is not recommended except for very small analyses. The BEAST-2.1.3 application available through the Discovery Environment (DE) or Agave API is much, much faster.

Why use this image?

All of the software in this image can easily be installed and run on a personal computer. However, if you want to do large analyses using the CyVerse high performance BEAST-2.1.3 application, you will need to have your data on the CyVerse Data Store. Once it is there, you may find it much easier to use this instance for preparing and evaluating your data, because you won't have to worry about it getting out of sync when you upload and download to your desktop. Maintaining all your data files on CyVerse also allows you to share data, analyses, and results with collaborators.

Using the BEAST-2.1.3 Accessories Image

Preliminaries

If you have used Atmosphere before, read through the Atmosphere manual.

Because most of the tools on this image require a graphical interface (GUI), you will need to use VNC to view the image. See the pages on how to use VNC.

This image is intended to work in conjunction with the BEAST-2.1.3 high performance app, available through the DE. Therefore, you will need to be able to move data back and forth between your Atmosphere instance and the CyVerse Data Store. To do this, you can either use iDROP Desktop (installed on the image) or create a volume.

Quick Start

• Make sure any data you need is on the CyVerse Data Store. See Manage Data on the CyVerse website for the methods to use.
• Log in to Atmosphere and select the image named "BEAST-2.1.3 Accessories". For most uses, a tiny instance will suffice, but if you want to work with larger datasets, you may consider spinning up a small or medium image.
• Use VNC to access the image.
• Open the README file on the Desktop for instructions on using the image.
• Use iDROP desktop or a volume to download the data you need to your instance.
• Use one of the applications listed below.

Available applications

See the tutorial links below for guidance on how to use these applications. The first six are distributed as part of BEAST. Tracer and FigTree are distributed separately, but can be used with BEAST.

1. BEAST

Bayesian Evolutionary Analysis Sampling Trees See the BEAST2 wiki main page for more information.

You can run BEAST directly in this instance for small analyses, but for most analyses it is recommended that you use the BEAST-2.1.3 HPC application.

• To run BEAST, click on the BEAST folder on the desktop and then double-click on beast. Be sure your XML file is available for input.

If you use BEAST, please cite:

Bouckaert R, Heled J, Kühnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) "BEAST2: A software platform for Bayesian evolutionary analysis". PLOS Computational Biogogy 10(4): e1003537, 2014. doi:10.1371/journal.pcbi.1003537 full text

2. BEAUti

A simple user interface for creating input files to run BEAST. See the BEAUti wiki page.

BEAUti will import data in NEXUS format, allow you to select various models and options and generate an XML file ready for use as input in BEAST.

• To run BEAUti, click on the BEAST folder on the desktop and then double-click on beauti.

3. DensiTree

A program for visualizing the information in a sample of trees produced by BEAST. See the DensiTree web page and DensiTree How To's.

• To run DensiTree, click on the BEAST folder on the desktop and then double-click on densitree.

4. LogCombiner

A program to combine log and tree files from multiple runs of BEAST. No manual is available for LogCombiner, but it should be more or less self-evident.

• To run LogCombiner, click on the BEAST folder on the desktop and then double-click on logcombiner.

5. TreeAnnotator

A program for summarizing the information in a sample of trees produced by BEAST. See the TreeAnnotator wiki page for more details.

• To run TreeAnnotator, click on the BEAST folder on the desktop and then double-click on treeannotator.

6. Other

The executables addonmanager.exe and appstore.exe are also available as part of the BEAST package, but are not necessary for common BEAST workflows.

7. Tracer

A program for analysing results from Bayesian MCMC programs such as BEAST and MrBayes_mpi_basic-3.2.3.

"Tracer is a program for analyzing the trace files generated by Bayesian MCMC runs (that is, the continuous parameter values sampled from the chain). It can be used to analyze runs of BEAST, MrBayes, LAMARC, and possibly other MCMC programs."

At present there is no detailed manual for this application. See the Tracer home page for basic instructions.

• To run Tracer, click on the BEAST folder on the desktop.

8.  FigTree

A program for viewing trees including summary information produced by TreeAnnotator.

• To run FigTree, click on the BEAST folder on the desktop.