MaxAlign: maximizing usable data in an alignment

Background: The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment. Results: MaxAlign is a program that optimizes the alignment prior to such analyses. Specifically, it maximizes the number of nucleotide (or amino acid) symbols that are present in gap-free columns – the alignment area – by selecting the optimal subset of sequences to exclude from the alignment. MaxAlign can be used prior to phylogenetic and bioinformatical analyses as well as in other situations where this form of alignment improvement is useful. In this work we test MaxAlign's performance in these tasks and compare the accuracy of phylogenetic estimates including and excluding gapped columns from the analysis, with and without processing with MaxAlign. In this paper we also introduce a new simple measure of tree similarity, No...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Rodrigo Gouveia-Oliveira, Peter Wad Sackett, Anders Gorm Pedersen
• Keywords: BMCBI 2007, Phylogenetic, Protein Sequences, Sequences