The Exelixis Lab

Enabling Research in Evolutionary Biology

Evolutionary Placement Algorithm (EPA)

Latest code download

The EPA is part of standard RAxML, so you will need to download the latest RAxML version. Get the most up-to-date RAxML version from github.

User Support

Please send all your questions and feature request to the RAxML google group. Before posting, keep in mind that a google group actually has a search function! Emails to Exelixis lab members regarding RAxML will not be answered. Messages posted via github will also not be answered.

Web-Servers for evolutionary placement of short reads

Web-Servers for phylogenetic placement of short sequence reads (including alignment and visualization tools):

Graphical User Interface (GUI)

Denis Krompass, our former Master's student has put together JAVA-based GUI packages for running and analyzing short read placement runs with the RAxML EPA algorithm described in this paper

This stand-alone GUI is similar in functionality to the EPA web-server here. It also allows you to build reference trees with RAxML for the original full-length sequence alignment

Just download the file (this may take some time), then unzip it: "unzip" then change to the directory: "cd RAxML_Workbench" and then start the GUI by typing: "java -jar RAxML_Worbench.jar"

Here is a screenshot of the GUI: