RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits

RibAlign serves two purposes: First, it provides a fast and scalable database that has been specifically adapted to eubacterial ribosomal protein sequences and second, it provides sophisticated import and export capabilities. This includes semi-automatic extraction of ribosomal protein sequences from whole-genome GenBank and FASTA files as well as exporting aligned, concatenated and filtered sequence files that can directly be used in conjunction with the PHYLIP and MrBayes phylogenetic reconstruction programs.Up to now, phylogeny based on concatenated ribosomal protein sequences is hampered by the limited set of sequenced genomes and high computational requirements. However, hundreds of full and draft genome sequencing projects are on the way, and advances in cluster-computing and algorithms make phylogenetic reconstructions feasible even with large alignments of concatenated marker genes. RibAlign is a first step in this direction and may be particularly interesting to scientists involved in whole genome sequencing of representatives of new or sparsely studied eubacterial phyla. RibAlign is available at http://www.megx.net/ribalign webciteAnalysis of 16S ribosomal rRNA (rRNA) sequences is currently the de-facto gold standard for the assessment of phylogenetic relationships among prokaryotes. There are various reasons that have made the 16S rRNA gene the first choice as a phylogenetic marker, such as the presence of positions with different evolutionary rates, its universal occurrence within prokaryotes, its reasonable information content, a length that was suitable for complete sequencing when the technique started, knowledge about its secondary structure that helps with alignments and finally the presence of a comprehensive database of more than hundred thousand sequences [1]. With ARB [2], there is also a well-curated 16S rRNA database with a curated alignment and a program suite for phylogenetic reconstructions available that has gained broad acceptance among s