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Algorithms for Molecular Biology BioMed Central Short report Open Access Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family 1 2 3,4 Holger Wagner , Burkhard Morgenstern* and Andreas Dress Address: 1FSPM, Faculty of Mathematics, Bielefeld University, Postfach 100131, D-33501 Bielefeld, Germany, 2Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr. 1, D-37077 Göttingen, 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