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Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise

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. Green open access

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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.

Type: Article
Title: Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1186/1471-2148-8-179
Publisher version: http://dx.doi.org/10.1186/1471-2148-8-179
Language: English
Additional information: PMCID: PMC2443136 © 2008 Dessimoz and Gil; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: Algorithms, Evolution, Molecular, Models, Statistical, Phylogeny, Sequence Alignment, Sequence Analysis, Protein
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: https://discovery.ucl.ac.uk/id/eprint/1404282
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