Fast and accurate estimation of the covariance between pairwise maximum likelihood distances
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...
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2014-09-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/583.pdf |
| _version_ | 1797425764263526400 |
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| author | Manuel Gil |
| author_facet | Manuel Gil |
| author_sort | Manuel Gil |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T08:19:49Z |
| format | Article |
| id | doaj.art-9b6e626c9b264740891f845ec87ecf5b |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T08:19:49Z |
| publishDate | 2014-09-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-9b6e626c9b264740891f845ec87ecf5b2023-12-02T21:50:35ZengPeerJ Inc.PeerJ2167-83592014-09-012e58310.7717/peerj.583583Fast and accurate estimation of the covariance between pairwise maximum likelihood distancesManuel Gil0Institute of Molecular Life Sciences, University of Zurich, Zurich, SwitzerlandPairwise 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.https://peerj.com/articles/583.pdfMaximum likelihoodPairwise distanceCovarianceCorrelationAlignment |
| spellingShingle | Manuel Gil Fast and accurate estimation of the covariance between pairwise maximum likelihood distances PeerJ Maximum likelihood Pairwise distance Covariance Correlation Alignment |
| title | Fast and accurate estimation of the covariance between pairwise maximum likelihood distances |
| title_full | Fast and accurate estimation of the covariance between pairwise maximum likelihood distances |
| title_fullStr | Fast and accurate estimation of the covariance between pairwise maximum likelihood distances |
| title_full_unstemmed | Fast and accurate estimation of the covariance between pairwise maximum likelihood distances |
| title_short | Fast and accurate estimation of the covariance between pairwise maximum likelihood distances |
| title_sort | fast and accurate estimation of the covariance between pairwise maximum likelihood distances |
| topic | Maximum likelihood Pairwise distance Covariance Correlation Alignment |
| url | https://peerj.com/articles/583.pdf |
| work_keys_str_mv | AT manuelgil fastandaccurateestimationofthecovariancebetweenpairwisemaximumlikelihooddistances |