Jonathan Eisen is happy to have published a new paper in Genome Biology, and Larry Moran thinks it's a good one. The authors, including Martin Wu, have written a software tool called AMPHORA that "can be used to build phylogenetic trees based on concatenated alignments of housekeeping proteins and also for metagenomic phylotyping using a diversity of protein markers." The gold standard of bacterial phylogeny, the SSU rRNA gene, isn't all that great for classifying bacterial species, says Moran. Eisen's method "resolves many groups that are unresolvable using the SSU rRNA tree. In some cases this tree reveals species that have been incorrectly assigned to higher taxa," he writes at Sandwalk.
A New Way to Classify Bacteria
Oct 17, 2008