The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

The box below searches only this space.
To search the entire iPlant wiki, enter your query in the box at the upper right.

 

 

Skip to end of metadata
Go to start of metadata

BEAST2 on CyVerse UK

Community rating: ?????

This is BEAST version 2.4.3 on the CyVerse UK hardware (12 cpus, 256 GB per job). It is software for Bayesian analysis of molecular sequences using MCMC. See http://beast2.org for more info.

Quick Start

  • This is a fairly simple app in terms of inputs and outputs, all it needs is a BEAST batch XML file which contains a sequence alignment and all options necessary for the program. See the example file in the example data. Also see the detailed guides on this file format here: http://beast2.org/tutorials/

Test Data

Icon

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> BEAST2_uk

Input File(s)

Only one file is necessary, the alignment and option xml file.

Output Files

  • beast.err, beast.log, beast.out - standard error, out and log
  • filename.log - log file of this run
  • filename.ops - cpu operations log of this run
  • filename.trees - all trees produced during the run

Other files may appear depending on your model, partitions, options etc...

Tool Source for App

https://github.com/CompEvol/beast2

 

  • No labels