The webserver implementation of the AMPHORA2 workflow for phylogenetic analysis of metagenomic shotgun sequencing data and genomic data

AmphoraNet uses 31 bacterial and 104 archaeal protein coding marker genes for metagenomic and genomic phylotyping. Most of these are single copy genes, therefore AmphoraNet is suitable for estimating the taxonomic composition of bacterial and archaeal communities from metagenomic shotgun sequencing data.

FASTA file (max size: 300 MB)
Marker genes:           

Using AmphoraNet step by step

  1. Upload a metagenomic or genomic sequence file in FASTA or FASTAQ format and at most 300 MB size. Sample input file (HMP - buccal mucosa metagenome). Other input files.
  2. Choose the type of your input data: DNA sequence or amino acid sequence.
  3. Choose the type of the marker genes you would like to search: bacteria, archaea or both.
  4. Click the "Check values" button. If everything is OK then click the "Schedule job" button.
  5. Next you are redirected to a unique page that you should bookmark or update later. The results will appear on this unique page when the job is finished. Ideally you will get an answer in 10-30 minutes.
  6. If your request is ready you can download three files on your unique page: an input file, a marker genes file and a results file. The marker genes file contains sequences of the phylogenetic marker genes found by AmphoraNet. The results file is tab-delimited and contains phylotypes for each identified phylogenetic marker gene (the numbers within the parentheses are the confidence scores).
    Sample output file (HMP - buccal mucosa metagenome). Other output files.
  7. Visualize the output file: AmphoraVizu.

More details and help

The AmphoraNet webserver is a web interface to the AMPHORA2 workflow of Wu and Scott, that is based on the AMPHORA suite of programs by Wu and Eisen. For more details please check our publication and presentation:

AmphoraNet uses the default options of AMPHORA2. If you have any questions or ideas related to AmphoraNet, please feel free contact us (, Csaba Kerepesi), or visit the AmphoraNet support forum and the AmphoraNet forum topic on Biostars.

Terms of use

You can use this service only if you accept the following terms: We do not guarantee anything about this service: We do not state anything about the usability of this service, and we do not state that the results that we may return can be used for any purpose. We cannot guarantee that this service will be available in the future, and we cannot guarantee that your query would generate any output at all.

Privacy: We will not give out your data to anyone, and, regularly, only you can retrieve the results to your query using the unique webpage identifier generated for you. However, we cannot guarantee that others do not intercept the traffic between you and our server. Therefore, do not use our webserver for proprietary data analysis, we cannot guarantee the data integrity and safety for you.

Citation requirement: If you publish anything using the output of AmphoraNet webserver, you are asked to cite the following publication, and you are also suggested to refer to the web address of our webservice:

Csaba Kerepesi, Dániel Bánky, Vince Grolmusz, AmphoraNet: The webserver implementation of the AMPHORA2 metagenomic workflow suite, Gene, Volume 533, Issue 2, 10 January 2014, Pages 538-540, ISSN 0378-1119,