UT-Austin Computational Phylogenetics Software

utcs Phylogenetics

Research · Publications ·

Software

· People · Datasets

SEPP

Overview

SATé-enabled phylogenetic placement (SEPP) is a software package for phylogenetic placement.

Acquiring

Currently SEPP is available for download and installation on Linux and Mac machines. Linux and Mac users are encouraged to download and install SEPP on their machines. Windows users (or Mac and Linux users who have problems with the installation) can use our VM image running Ubuntu 11.10 with SEPP already installed on it.

Downlaod and Install:
To download and to see details on how to install and run latest version of SEPP, please see our github repository. The README file on the github repository has instructions for installation. Alternatively, consult the tutorial provided below.
If you are interested in the version corresponding to the PSB paper, pleaser refer to Software section of the Supplementary Materials for the PSB Publication page.

Virtual Machine:

The VM image is available here for download. Note that the VM image is 1.7 GB and can take a long time to download. Once the image is downloaded, you need to run it using a virtualization product (such as VirtualBox). Once VM is running, you can login using (username: ubuntu, password: reverse). SEPP is already installed on the VM machine, so you can simply proceed by opening a terminal and running SEPP using run_sepp.py.

Tutorial

A tutorial describing how SEPP works is is available here. Note that the github repository also has the tutorial included, and the github version might be more up-to-date.

Publication

SEPP: SATé-Enabled Phylogenetic Placement. Pac Symp Biocomput (PSB) 2012:247-58 (PubMed).

Supplementary Materials for the PSB Paper

Please see this page for data corresponding to our PSB paper.

Contact

SEPP is under active research development at UTCS by the Warnow Lab (and especially with her PhD students Siavash Mirarab and Nam Nguyen). We welcome research collaborations. Please contact Tandy Warnow directly by email (not by phone, please).