Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family

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 bootstrapping frequencies, the so-called safe branches. We show that this instability is caused by the fact that both, CLUSTAL W as well as DIALIGN, apparently get "confused" by sequence repeats in some of the ABC-transporter. To deal with such problems, two new DIALIGN options are introduced that prove helpful in our context, the "exclude-...

• Type: Journal
• Year: 2008
• Where: ALMOB
• Authors: Holger Wagner, Burkhard Morgenstern, Andreas W. M. Dress
• Keywords: ALMOB 2008, Intrinsic Phylogenetic Instability, Phylogeny Reconstruction, Sequence-based Phylogeny Reconstruction