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Fast and accurate estimation of the covariance between pairwise maximum likelihood distances.

ABSTRACT: Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989) which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error.

SUBMITTER: Gil M

PROVIDER: S-EPMC4179615 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Fast and accurate estimation of the covariance between pairwise maximum likelihood distances.

Gil Manuel M

PeerJ 20140925

Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum ...[more]

PMID: 25279263

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Dataset Information

Fast and accurate estimation of the covariance between pairwise maximum likelihood distances.

Publications

Fast and accurate estimation of the covariance between pairwise maximum likelihood distances.

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