Difference between revisions of "PartitionFinder"

Revision as of 15:26, 5 July 2012

Description

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PartitionFinder and PartitionFinderProtein are free open source programs for selecting best-fit partitioning schemes and models of molecular evolution for nucleotide and amino acid alignments. They take the hard work out of comparing partitioning schemes, and are useful in any situation where you wish to compare or select partitioning schemes or models of molecular evolution. Both programs come together as a single download. Click below to get the appropriate download for your system. Template:App Location

Available versions

1.0.0

Running the application using modules

To use partitionfinder with the environment modules system at HPC the following commands are available:

Get module information for partitionfinder:

$module spider partitionfinder

Load the default application module:

$module load partitionfinder

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

HPC_PARTITIONFINDER_DIR - directory where partitionfinder is located.

How To Run

PartitionFinder is a python application, so the direct way to run it is to use python $HPC_PARTITIONFINDER_DIR/PartitionFinder.py -n X DIRECTORY once the partitionfinder module is loaded where "X" is the number of compute cores requested in the job script, ... are any addition options and DIRECTORY is the directory with the configuration and input files. However, we have a convenience partitionfinder script that allows you to run PartitionFinder directly as partitionfinder -n X DIRECTORY.

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 {{#if: {{#var: exe}}|==How To Run==
-PathFinder is a python application, so the direct way to run it is to use <code>python $HPC_PATHFINDER_DIR/PathFinder.py -n X DIRECTORY</code> once the <code>pathfinder</code> module is loaded where "X" is the number of compute cores requested in the job script, ... are any addition options and DIRECTORY is the directory with the configuration and input files. However, we have a convenience <code>pathfinder</code> script that allows you to run PathFinder directly as <code>pathfinder -n X DIRECTORY</code>.
+PartitionFinder is a python application, so the direct way to run it is to use <code>python $HPC_PARTITIONFINDER_DIR/PartitionFinder.py -n X DIRECTORY</code> once the <code>partitionfinder</code> module is loaded where "X" is the number of compute cores requested in the job script, ... are any addition options and DIRECTORY is the directory with the configuration and input files. However, we have a convenience <code>partitionfinder</code> script that allows you to run PartitionFinder directly as <code>partitionfinder -n X DIRECTORY</code>.
 |}}
 <!--Configuration-->