Difference between revisions of "PartitionFinder"

Latest revision as of 16:57, 21 August 2022

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.

Environment Modules

Run module spider partitionfinder to find out what environment modules are available for this application.

System Variables

HPC_PARTITIONFINDER_DIR - installation directory

How To Run

Run PartitionFinder programs for nt or aa model analysis respectively as

PartitionFinder.py -p X DIRECTORY

and

PartitionFinderProtein.py -p X DIRECTORY

once the partitionfinder module is loaded where "X" is the number of compute cores requested in the job script and "DIRECTORY" is the full path to a folder containing a configuration file (partition_finder.cfg) and a nucleotide or aminoacid alignment in Phylip format.

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.

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Bioinformatics]][[Category:Phylogenetics]]
+[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]][[Category:Genomics]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|partitionfinder}}
@@ Line 24: / Line 24: @@
 <!--Modules-->
-{{#if: {{#var: mod}}|==Execution Environment and Modules==
+==Environment Modules==
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
+==System Variables==
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 <!--Run-->
 {{#if: {{#var: exe}}|==How To Run==
-PartitionFinder is a python application, so the direct way to run it is to use <code>python $HPC_PARTITIONFINDER_DIR/PartitionFinder.py -p X DIRECTORY</code> or <code>python $HPC_PARTITIONFINDER_DIR/PartitionFinderProtein.py -p X DIRECTORY</code> for nt or aa models respectively 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 scripts that allow you to run PartitionFinder directly for either nt or aa analysis as <code>partitionfindernt -p X NUCLEOTIDE_DIRECTORY</code> or <code>partitionfinderaa -p X AMINOACID_DIRECTORY</code> once the <code>partitionfinder</code> module is loaded.
+Run PartitionFinder programs for nt or aa model analysis respectively as
+ PartitionFinder.py -p X DIRECTORY
+and
+ PartitionFinderProtein.py -p X DIRECTORY
+once the <code>partitionfinder</code> module is loaded where "X" is the number of compute cores requested in the job script and "DIRECTORY" is the full path to a folder containing a configuration file (partition_finder.cfg) and a nucleotide or aminoacid alignment in Phylip format.
 |}}
 <!--Configuration-->