Usage

Currently, the following tools are supported, and are bundled with the SATe distribution:

• ClustalW 2.0.12
• MAFFT 6.717
• MUSCLE 3.7
• OPAL 1.0.3
• PRANK 100311
• RAxML 7.2.6
• FastTree 2.1.4

Note: By default, SATe uses your home directory as the location for temporary files. It is a violation of HPC policy for jobs to write to your home directory. It is critical that you include the --temporaries= flag in your SATe command line to provide an alternative path for the temp files. PBS provides the $TMPDIR variable for you, and this is an excellent option. See example submission script. Another convenient variable you could use is $PBS_O_WORKDIR, something like --temporaries=$PBS_O_WORKDIR/temp would work well too.

For all command line options, run:

run_sate.py -h