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Summary
Phylogenetic trees depicting the evolutionary relatedness of different species or groups of species are often determined by analyzing the similarities and differences between genetic sequences. The problems involved—sequence alignment and phylogenetic inference—are among the oldest in bioinformatics (1, 2) and are still much studied (3–7). As was noticed early on, however, alignment and phylogenetic inference are not separate problems but should be seen as two parts of one question: the detection of sequence homology (8). On page 1561 of this issue, Liu et al. (9) describe a new approach for the coestimation of phylogenetic trees and sequence alignments for very large data sets.
