Dessimoz, C; Gil, M; (2008) Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise. BMC Evolutionary Biology , 8 , Article 179. 10.1186/1471-2148-8-179.

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Abstract

The estimation of a distance between two biological sequences is a fundamental process in molecular evolution. It is usually performed by maximum likelihood (ML) on characters aligned either pairwise or jointly in a multiple sequence alignment (MSA). Estimators for the covariance of pairs from an MSA are known, but we are not aware of any solution for cases of pairs aligned independently. In large-scale analyses, it may be too costly to compute MSAs every time distances must be compared, and therefore a covariance estimator for distances estimated from pairs aligned independently is desirable. Knowledge of covariances improves any process that compares or combines distances, such as in generalized least-squares phylogenetic tree building, orthology inference, or lateral gene transfer detection.

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