Stability of multiple alignments and phylogenetic trees an analysis of ABC-transporter proteins family 英文参考文献.docVIP

Algorithms for Molecular Biology BioMedCentral Short report Open Access Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family Holger Wagner1, Burkhard Morgenstern*2 and Andreas Dress3,4 Address: 1FSPM, Faculty of Mathematics, Bielefeld University, Postfach 100131, D-33501 Bielefeld, Germany, 2Institute of Microbiology and Genetics, University of G?ttingen, Goldschmidtstr. 1, D-37077 G?ttingen, Germany, 3CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, 200031 Shanghai, PR China and 4Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22 – 26, D-04103 Leipzig, Germany Email: Holger Wagner - h_wagner@t-online.de; Burkhard Morgenstern* - bmorgen@gwdg.de; Andreas Dress - andreas@ * Corresponding author Published: 6 November 2008 Received: 30 April 2008 Accepted: 6 November 2008 Algorithms for Molecular Biology 2008, 3:15 doi:10.1186/1748-7188-3-15 This article is available from: /content/3/1/15 ? 2008 Wagner et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Sequence-based phylogeny reconstruction is a fundamental task in Bioinformatics. Practically all methods for phylogeny reconstruction are based on multiple alignments. The quality and stability of the underlying alignments is therefore crucial for phylogenetic analysis. Results: In this short report, we investigate alignments and alignment-based phylogenies constructed for a set of 22 ABC transporters using CLUSTAL W and DIALIGN. Comparing the 22 one-out phylogenies one can obtain for this sequence set, some intrinsic phylogenetic instability is observed — even if attention is restricted to branches with high boo