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Coalescent: an open-source and scalable framework for exact calculations in coalescent theory
BACKGROUND: Currently, there is no open-source, cross-platform and scalable framework for coalescent analysis in population genetics. There is no scalable GUI based user application either. Such a framework and application would not only drive the creation of more complex and realistic models but al...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575375/ https://www.ncbi.nlm.nih.gov/pubmed/23033878 http://dx.doi.org/10.1186/1471-2105-13-257 |
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author | Tewari, Susanta Spouge, John L |
author_facet | Tewari, Susanta Spouge, John L |
author_sort | Tewari, Susanta |
collection | PubMed |
description | BACKGROUND: Currently, there is no open-source, cross-platform and scalable framework for coalescent analysis in population genetics. There is no scalable GUI based user application either. Such a framework and application would not only drive the creation of more complex and realistic models but also make them truly accessible. RESULTS: As a first attempt, we built a framework and user application for the domain of exact calculations in coalescent analysis. The framework provides an API with the concepts of model, data, statistic, phylogeny, gene tree and recursion. Infinite-alleles and infinite-sites models are considered. It defines pluggable computations such as counting and listing all the ancestral configurations and genealogies and computing the exact probability of data. It can visualize a gene tree, trace and visualize the internals of the recursion algorithm for further improvement and attach dynamically a number of output processors. The user application defines jobs in a plug-in like manner so that they can be activated, deactivated, installed or uninstalled on demand. Multiple jobs can be run and their inputs edited. Job inputs are persisted across restarts and running jobs can be cancelled where applicable. CONCLUSIONS: Coalescent theory plays an increasingly important role in analysing molecular population genetic data. Models involved are mathematically difficult and computationally challenging. An open-source, scalable framework that lets users immediately take advantage of the progress made by others will enable exploration of yet more difficult and realistic models. As models become more complex and mathematically less tractable, the need for an integrated computational approach is obvious. Object oriented designs, though has upfront costs, are practical now and can provide such an integrated approach. |
format | Online Article Text |
id | pubmed-3575375 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-35753752013-02-20 Coalescent: an open-source and scalable framework for exact calculations in coalescent theory Tewari, Susanta Spouge, John L BMC Bioinformatics Software BACKGROUND: Currently, there is no open-source, cross-platform and scalable framework for coalescent analysis in population genetics. There is no scalable GUI based user application either. Such a framework and application would not only drive the creation of more complex and realistic models but also make them truly accessible. RESULTS: As a first attempt, we built a framework and user application for the domain of exact calculations in coalescent analysis. The framework provides an API with the concepts of model, data, statistic, phylogeny, gene tree and recursion. Infinite-alleles and infinite-sites models are considered. It defines pluggable computations such as counting and listing all the ancestral configurations and genealogies and computing the exact probability of data. It can visualize a gene tree, trace and visualize the internals of the recursion algorithm for further improvement and attach dynamically a number of output processors. The user application defines jobs in a plug-in like manner so that they can be activated, deactivated, installed or uninstalled on demand. Multiple jobs can be run and their inputs edited. Job inputs are persisted across restarts and running jobs can be cancelled where applicable. CONCLUSIONS: Coalescent theory plays an increasingly important role in analysing molecular population genetic data. Models involved are mathematically difficult and computationally challenging. An open-source, scalable framework that lets users immediately take advantage of the progress made by others will enable exploration of yet more difficult and realistic models. As models become more complex and mathematically less tractable, the need for an integrated computational approach is obvious. Object oriented designs, though has upfront costs, are practical now and can provide such an integrated approach. BioMed Central 2012-10-03 /pmc/articles/PMC3575375/ /pubmed/23033878 http://dx.doi.org/10.1186/1471-2105-13-257 Text en Copyright ©2012 Tewari and Spouge; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 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. |
spellingShingle | Software Tewari, Susanta Spouge, John L Coalescent: an open-source and scalable framework for exact calculations in coalescent theory |
title | Coalescent: an open-source and scalable framework for exact calculations in coalescent theory |
title_full | Coalescent: an open-source and scalable framework for exact calculations in coalescent theory |
title_fullStr | Coalescent: an open-source and scalable framework for exact calculations in coalescent theory |
title_full_unstemmed | Coalescent: an open-source and scalable framework for exact calculations in coalescent theory |
title_short | Coalescent: an open-source and scalable framework for exact calculations in coalescent theory |
title_sort | coalescent: an open-source and scalable framework for exact calculations in coalescent theory |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575375/ https://www.ncbi.nlm.nih.gov/pubmed/23033878 http://dx.doi.org/10.1186/1471-2105-13-257 |
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