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):
- advanced Swiss Server with pre-computed trees, please cite this paper when using it
- basic German Server without pre-computed trees, please cite this paper when using it
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 RAxML_Workbench_Linux.zip" 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:
