Jump to navigation Jump to search


amphora2 website  

An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.

AMPHORA2 is free software: you may redistribute it and/or modify its under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or any later version.

Environment Modules

Run module spider amphora2 to find out what environment modules are available for this application.

System Variables

  • HPC_AMPHORA2_DIR - installation directory
  • HPC_AMPHORA2_BIN - executable directory
  • HPC_AMPHORA2_DOC - documentation directory
  • HPC_AMPHORA2_EXE - test data directory
  • HPC_AMPHORA2_TAX- taxonomy data directory
  • HPC_AMPHORA2_TREE - tree data directory


If you publish research that uses amphora2 you have to cite it as follows:

Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28(7):1033-1034