Local and relaxed clocks, the best of both worlds

Fourment, M; Darling, AE

Local and relaxed clocks, the best of both worlds

Fourment, M

Darling, AE

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Publisher:: PeerJ
Publication Type:: Journal Article
Citation:: 2018
Issue Date:: 2018-07-03

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Field	Value	Language
dc.contributor.author	Fourment, M https://orcid.org/0000-0001-8153-9822	en_US
dc.contributor.author	Darling, AE https://orcid.org/0000-0003-2397-7925	en_US
dc.date.issued	2018-07-03	en_US
dc.identifier.citation	2018	en_US
dc.identifier.uri	http://hdl.handle.net/10453/136719
dc.description.abstract	<jats:p>Time-resolved phylogenetic methods use information about the time of sample collection to estimate the rate of evolution. Originally, the models used to estimate evolutionary rates were quite simple, assuming that all lineages evolve at the same rate, an assumption commonly known as the molecular clock. Richer and more complex models have since been introduced to capture the phenomenon of substitution rate variation among lineages. Two well known model extensions are the local clock, wherein all lineages in a clade share a common substitution rate, and the uncorrelated relaxed clock, wherein the substitution rate on each lineage is independent from other lineages while being constrained to fit some parametric distribution. We introduce a further model extension, called the flexible local clock (FLC), which provides a flexible framework to combine relaxed clock models with local clock models. We evaluate the flexible local clock on simulated and real datasets and show that it provides substantially improved fit to an influenza dataset. An implementation of the model is available for download from <jats:uri>https://www.github.com/4ment/flc</jats:uri>.</jats:p>	en_US
dc.publisher	PeerJ	en_US
dc.relation.isbasedon	10.7287/peerj.preprints.26744v1	en_US
dc.title	Local and relaxed clocks, the best of both worlds	en_US
dc.type	Journal Article
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - ithree - Institute of Infection, Immunity and Innovation
utslib.copyright.status	open_access
pubs.consider-herdc	true	en_US

Abstract:

Time-resolved phylogenetic methods use information about the time of sample collection to estimate the rate of evolution. Originally, the models used to estimate evolutionary rates were quite simple, assuming that all lineages evolve at the same rate, an assumption commonly known as the molecular clock. Richer and more complex models have since been introduced to capture the phenomenon of substitution rate variation among lineages. Two well known model extensions are the local clock, wherein all lineages in a clade share a common substitution rate, and the uncorrelated relaxed clock, wherein the substitution rate on each lineage is independent from other lineages while being constrained to fit some parametric distribution. We introduce a further model extension, called the flexible local clock (FLC), which provides a flexible framework to combine relaxed clock models with local clock models. We evaluate the flexible local clock on simulated and real datasets and show that it provides substantially improved fit to an influenza dataset. An implementation of the model is available for download from https://www.github.com/4ment/flc.

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http://hdl.handle.net/10453/136719