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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.

Required Modules


  • amphora2

System Variables

  • HPC_{{#uppercase:amphora2}}_DIR - installation directory
  • HPC_{{#uppercase:amphora2}}_BIN - executable directory
  • HPC_{{#uppercase:amphora2}}_DOC - documentation directory
  • HPC_{{#uppercase:amphora2}}_EXE - test data directory
  • HPC_{{#uppercase:amphora2}}_TAX- taxonomy data directory
  • HPC_{{#uppercase: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