The GAST algorithm assigns taxonomy to SSU sequences by comparing them to a set of reference sequences with known taxonomy. In the simplest terms, taxonomy is assigned to each query sequence based on the consensus of the nearest references sequences. The alignment distance between the query and references is also reported as a measure of how similar the query and reference sequences really are.
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Huse SM, Dethlefsen L, Huber JA, Mark Welch D, Relman DA, et al. (2008)
Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing.
PLoS Genetics 4: e1000255..