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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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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Libertas Academica
2013
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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 |
collection | PubMed |
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. |
format | Online Article Text |
id | pubmed-3869629 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Libertas Academica |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT roychoudhuryarindam approximatelikelihoodestimationofdivergencetimerangeusingacoalescentbasedmodel |