SEPP stands for "SATe-enabled Phylogenetic Placement", and addresses the problem of phylogenetic placement of short reads into reference alignments and trees.

• Version: 4.5.1
• Added: May, 2020
• Updated: December, 2021
• Link: https://github.com/smirarab/sepp

See versions of sepp which are available:

$ module avail sepp

Load one version into your environment and run it:

$ module load sepp/4.5.1
$ run_sepp.py -h

The general command for running SEPP is:

run_sepp.py -t <tree_file> -a <alignment_file> -f <fragment_file> -r <raxml_info_file> -A <alignment_set_size> -P <placement_set_size>

Note: please use the "-x" or "–cpu" options to set the number of CPUs for your SEPP run. This number should match the number of CPUs requested in your SBATCH allocation.

Notes from the sysadmin during installation:

$ sudo mkdir -p /export/apps/sepp/4.5.1
$ sudo chown aorth:aorth /export/apps/sepp/4.5.1
$ git clone https://github.com/smirarab/sepp.git -b 4.5.1 /export/apps/sepp/4.5.1
$ cd /export/apps/sepp/4.5.1
$ python3 -m venv venv
$ source venv/bin/activate
$ pip install --upgrade pip setuptools
$ python setup.py config -c
$ python setup.py install
$ sed -i 's?/usr/bin/env python?/usr/bin/env python3?' run_*.py split_sequences.py
$ sudo chown -R root:root /export/apps/sepp/4.5.1

Sepp's setup script wants to write the main.config file in the user's home directory or the source directory, so we need to clone the git repository to /export/apps where we intend to install it and then use the local (-c) config option.