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Approximate Likelihood Estimation of Divergence Time Range Using a Coalescent-based Model

We present an estimation of divergence time-range based on a coalescent model. This model sum the probability of coalescent trees, taking into account the effect of incomplete lineage sorting. Maximum likelihood estimate based on this model has been computed previously; however, a formula for diverg...

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Autor principal: RoyChoudhury, Arindam
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Libertas Academica 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3869629/
https://www.ncbi.nlm.nih.gov/pubmed/24367158
http://dx.doi.org/10.4137/EBO.S13080
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author RoyChoudhury, Arindam
author_facet RoyChoudhury, Arindam
author_sort RoyChoudhury, Arindam
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description We present an estimation of divergence time-range based on a coalescent model. This model sum the probability of coalescent trees, taking into account the effect of incomplete lineage sorting. Maximum likelihood estimate based on this model has been computed previously; however, a formula for divergence time-range estimate or confidence interval has never been presented for this model as the expression of the likelihood makes this estimation difficult to compute. Our formula for the divergence time-range estimate can be readily coded into a program. We did not use a simulation or resampling-based approach and therefore our method is fast and less computationally intensive. We demonstrate that our method is much faster and as accurate a simulation-based approach.
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spelling pubmed-38696292013-12-23 Approximate Likelihood Estimation of Divergence Time Range Using a Coalescent-based Model RoyChoudhury, Arindam Evol Bioinform Online Original Research We present an estimation of divergence time-range based on a coalescent model. This model sum the probability of coalescent trees, taking into account the effect of incomplete lineage sorting. Maximum likelihood estimate based on this model has been computed previously; however, a formula for divergence time-range estimate or confidence interval has never been presented for this model as the expression of the likelihood makes this estimation difficult to compute. Our formula for the divergence time-range estimate can be readily coded into a program. We did not use a simulation or resampling-based approach and therefore our method is fast and less computationally intensive. We demonstrate that our method is much faster and as accurate a simulation-based approach. Libertas Academica 2013-12-10 /pmc/articles/PMC3869629/ /pubmed/24367158 http://dx.doi.org/10.4137/EBO.S13080 Text en © 2013 the author(s), publisher and licensee Libertas Academica Ltd. This is an open-access article distributed under the terms of the Creative Commons CC-BY-NC 3.0 License.
spellingShingle Original Research
RoyChoudhury, Arindam
Approximate Likelihood Estimation of Divergence Time Range Using a Coalescent-based Model
title Approximate Likelihood Estimation of Divergence Time Range Using a Coalescent-based Model
title_full Approximate Likelihood Estimation of Divergence Time Range Using a Coalescent-based Model
title_fullStr Approximate Likelihood Estimation of Divergence Time Range Using a Coalescent-based Model
title_full_unstemmed Approximate Likelihood Estimation of Divergence Time Range Using a Coalescent-based Model
title_short Approximate Likelihood Estimation of Divergence Time Range Using a Coalescent-based Model
title_sort approximate likelihood estimation of divergence time range using a coalescent-based model
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3869629/
https://www.ncbi.nlm.nih.gov/pubmed/24367158
http://dx.doi.org/10.4137/EBO.S13080
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