The Data

The evolutionary distances are based on an analysis of SSU rRNA sequence data. The sequences are gathered from GenBank, the Ribosomal Database Project, and the database provided with the ARB software suite. A great deal of effort is put into keeping pace with sequences from new species published in the International Journal of Systematic and Evolutionary Microbiology. The same degree of effort is put into keeping abreast of the opinions of the authors contributing to Bergey's Manual of Systematic Bacteriology.
• Once gathered, the sequences are aligned in the ARB aligner, which allows users to take account of extensive secondary structure information about SSU rRNA when evaluating alignments. A mask is also applied to the alignments that restricts phylogenetic analysis to 1100 conserved positions in the Prokaryotic alignment.
• Aligned, masked sequence sets are saved and imported into PAUP*, where distance matrices are generated for each set. Since the sequences represent the entire spectrum of prokaryotic diversity, a simple model of evolution, the Jukes-Cantor model, is used to correct the measured distances between the sequences.