A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes

被引：60

作者：

Peplies, Joerg ^{[2
]}

Kottmann, Renzo ^{[1
,4
]}

Ludwig, Wolfgang ^{[3
]}

Gloeckner, Frank Oliver ^{[1
,4
]}

机构：

[1] Max Planck Inst Marine Microbiol, Microbial Genom Grp, D-28359 Bremen, Germany

[2] Ribocon Gmbh, D-28359 Bremen, Germany

[3] Tech Univ Munich, Lehrstuhl Mikrobiol, D-85350 Freising Weihenstephan, Germany

[4] Jacobs Univ Bremen gGmbH, D-28759 Bremen, Germany

来源：

SYSTEMATIC AND APPLIED MICROBIOLOGY | 2008年 / 31卷 / 04期

关键词：

Phylogenetic analysis; Tree reconstruction; Ribosomal RNA; Alignment; Standardization;

D O I：

10.1016/j.syapm.2008.08.003

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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. (C) 2008 Elsevier GmbH. All rights reserved.

引用

页码：251 / 257

页数：7

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