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A Standard Operating Procedure for Phylogenetic Inference (SOPPI)

Phylogenetic analysis is currently used worldwide for taxonomic classification and identification of microorganisms. Despite the countless trees that have been reconstructed and published over the last decades, no user-friendly compilation of recommendations to standardize the data analysis and tree reconstruction process have been published, so far.

This Standard Operating Procedure for Phylogenetic Inference (SOPPI) offers a helping hand in working through the process of sampling in the field to phylogenetic tree reconstruction and publication. 

SOPPI is not meant to be authoritative or comprehensive, but should help to make phylogenetic inference and diversity analysis more reliable and comparable among different labs.

SOPPI is mainly focused on using the ribosomal RNA as a universal phylogenetic marker, but the principles and recommendations can be applied to any valid marker gene.


Feedback and suggestions from the community are welcome to further improve these guidelines!

Please contact contact (at) and use 'SOPPI' in the subject line.

Topics addressed by SOPPI

  • Sampling (contextual data aquisition)
  • Sequencing
  • Alignment
  • Tree Reconstruction
  • Presentation of Trees
  • Documentation
  • Sequence submission and access to sequences
  • Plus an example for your 'Material & Methods' section!

Citation & Paper

Peplies, J., R. Kottmann, W. Ludwig, and F. O. Glöckner. 2008. A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes. Syst Appl Microbiol 31:251-257


Updates and Suggestions

First of all - many thanks for all the feedback concerning the SOPPI paper!

1. Frank Oliver Glöckner (19.09.2008):

The statement that RDP II provides only bacterial sequences is not longer true, with RDP release 10 also Archaea have been included.

2. Alexandros Stamatakis ( personal webpage) (19.09.2008):

The Bayesian Inference is missing in the SOPPI paper. A good tool which can be also used in combination with ARB is MrBayes

A nice paper to standardize the reporting of phylogenies entitled "Minimum Information about a
Phylogenetic Analysis (MIAPA)" was written by Jim Leebens-Mack and published in 2006 in the OMICS journal

Another nice paper about methods used by the community entitled "Methodology capture: discriminating between the "best" and the rest of
community practice" was published just recently in BMC Bioinformatics by James M Eales.

3. Rogan Rattrey & Pat Schloss (22.09.2008):

An automatic pipeline for alignments and tree based rRNA taxonomy for SSU has been published by Eisen et al. in PLoS one.