PartitionFinder
Description
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.
Execution Environment and 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 -p X DIRECTORY or python $HPC_PARTITIONFINDER_DIR/PartitionFinderProtein.py -p X DIRECTORY for nt or aa models respectively 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 scripts that allow you to run PartitionFinder directly for either nt or aa analysis as partitionfindernt -p X NUCLEOTIDE_DIRECTORY or partitionfinderaa -p X AMINOACID_DIRECTORY once the partitionfinder module is loaded.
Citation
If you publish research that uses partitionfinder you have to cite it as follows: Please cite Lanfear et al. (2012) if you use the tool for published research.