A conditional approach to the detection of correlated mutations

摘要

Some genomes mutate quickly. Studying their mutation process may allow us to understand the selection pressures these genomes are undergoing. Considering simultaneous mutations at several sites may provide insights into protein structure. We consider the situation where the frequency table for the aminoacid pairs can be summarized by a 2 * 2 table. We develop a test for mutational linkage between two positions conditionally on the consensus pair. We illustrate the use of this test with sequences from the V3 loop of the envelope gene from the human immunodeficiency virus.