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Fast "coalescent" simulation
BACKGROUND: The amount of genome-wide molecular data is increasing rapidly, as is interest in developing methods appropriate for such data. There is a consequent increasing need for methods that are able to efficiently simulate such data. In this paper we implement the sequentially Markovian coalesc...
Autores principales: | , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2006
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1458357/ https://www.ncbi.nlm.nih.gov/pubmed/16539698 http://dx.doi.org/10.1186/1471-2156-7-16 |
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author | Marjoram, Paul Wall, Jeff D |
author_facet | Marjoram, Paul Wall, Jeff D |
author_sort | Marjoram, Paul |
collection | PubMed |
description | BACKGROUND: The amount of genome-wide molecular data is increasing rapidly, as is interest in developing methods appropriate for such data. There is a consequent increasing need for methods that are able to efficiently simulate such data. In this paper we implement the sequentially Markovian coalescent algorithm described by McVean and Cardin and present a further modification to that algorithm which slightly improves the closeness of the approximation to the full coalescent model. The algorithm ignores a class of recombination events known to affect the behavior of the genealogy of the sample, but which do not appear to affect the behavior of generated samples to any substantial degree. RESULTS: We show that our software is able to simulate large chromosomal regions, such as those appropriate in a consideration of genome-wide data, in a way that is several orders of magnitude faster than existing coalescent algorithms. CONCLUSION: This algorithm provides a useful resource for those needing to simulate large quantities of data for chromosomal-length regions using an approach that is much more efficient than traditional coalescent models. |
format | Text |
id | pubmed-1458357 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2006 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-14583572006-05-08 Fast "coalescent" simulation Marjoram, Paul Wall, Jeff D BMC Genet Software BACKGROUND: The amount of genome-wide molecular data is increasing rapidly, as is interest in developing methods appropriate for such data. There is a consequent increasing need for methods that are able to efficiently simulate such data. In this paper we implement the sequentially Markovian coalescent algorithm described by McVean and Cardin and present a further modification to that algorithm which slightly improves the closeness of the approximation to the full coalescent model. The algorithm ignores a class of recombination events known to affect the behavior of the genealogy of the sample, but which do not appear to affect the behavior of generated samples to any substantial degree. RESULTS: We show that our software is able to simulate large chromosomal regions, such as those appropriate in a consideration of genome-wide data, in a way that is several orders of magnitude faster than existing coalescent algorithms. CONCLUSION: This algorithm provides a useful resource for those needing to simulate large quantities of data for chromosomal-length regions using an approach that is much more efficient than traditional coalescent models. BioMed Central 2006-03-15 /pmc/articles/PMC1458357/ /pubmed/16539698 http://dx.doi.org/10.1186/1471-2156-7-16 Text en Copyright © 2006 Marjoram and Wall; 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 Marjoram, Paul Wall, Jeff D Fast "coalescent" simulation |
title | Fast "coalescent" simulation |
title_full | Fast "coalescent" simulation |
title_fullStr | Fast "coalescent" simulation |
title_full_unstemmed | Fast "coalescent" simulation |
title_short | Fast "coalescent" simulation |
title_sort | fast "coalescent" simulation |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1458357/ https://www.ncbi.nlm.nih.gov/pubmed/16539698 http://dx.doi.org/10.1186/1471-2156-7-16 |
work_keys_str_mv | AT marjorampaul fastcoalescentsimulation AT walljeffd fastcoalescentsimulation |