A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes.
Phylogenetic analysis is currently used worldwide for taxonomic classification and identification of microorganisms. However, despite the countless trees that have been reconstructed and published in recent decades, so far, no user-friendly compilation of recommendations to standardize the data analysis and tree reconstruction process has been published. Consequently, this standard operating procedure for phylogenetic inference (SOPPI) offers a helping hand for working through the process from sampling in the field to phylogenetic tree reconstruction and publication. It is not meant to be authoritative or comprehensive, but should help to make phylogenetic inference and diversity analysis more reliable and comparable between different laboratories. It 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 scientific community are welcome in order to improve these guidelines further. Any updates will be made available on the SILVA webpage at http://www.arb-silva.de/projects/soppi.
Peplies
Jörg
J
Ribocon GmbH, D-28359 Bremen, Germany.
Kottmann
Renzo
R
Ludwig
Wolfgang
W
Glöckner
Frank Oliver
FO
D001419:Bacteria / Q000145:classification* / Q000235:genetics; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods* / Q000592:standards; D030561:Databases, Nucleic Acid; D020459:Genes, rRNA; D005819:Genetic Markers; D010802:Phylogeny; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods* / Q000592:standards
D005819:Genetic Markers