Freeing phylogenies from artifacts of alignment.

Widely used methods for phylogenetic inference, both those that require and those that produce alignments, share certain weaknesses. These weaknesses are discussed, and a method that lacks them is introduced. For each pair of sequences in the data set, the method utilizes both insertion-deletion and amino acid replacement information to estimate a pairwise evolutionary distance. It is also possible to allow regional heterogeneity of replacement rates. Because a likelihood framework is adopted, the standard deviation of each pairwise distance can be estimated. The distance matrix and standard error estimates are used to infer a phylogenetic tree. As an example, this method is used on 10 widely diverged sequences of the second largest RNA polymerase subunit. A pseudo-bootstrap technique is devised to assess the validity of the inferred phylogenetic tree.