Tools for simulating evolution of aligned genomic regions with integrated parameter estimation

Controlled simulations of genome evolution are useful for benchmarking tools. However, many simulators lack extensibility and cannot measure parameters directly from data. These issues are addressed by three new open-source programs: GSIMULATOR (for neutrally evolving DNA), SIMGRAM (for generic stru...

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Detalles Bibliográficos
Autores principales: Varadarajan, Avinash, Bradley, Robert K, Holmes, Ian H
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760874/
https://www.ncbi.nlm.nih.gov/pubmed/18840304
http://dx.doi.org/10.1186/gb-2008-9-10-r147
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author Varadarajan, Avinash
Bradley, Robert K
Holmes, Ian H
author_facet Varadarajan, Avinash
Bradley, Robert K
Holmes, Ian H
author_sort Varadarajan, Avinash
collection PubMed
description Controlled simulations of genome evolution are useful for benchmarking tools. However, many simulators lack extensibility and cannot measure parameters directly from data. These issues are addressed by three new open-source programs: GSIMULATOR (for neutrally evolving DNA), SIMGRAM (for generic structured features) and SIMGENOME (for syntenic genome blocks). Each offers algorithms for parameter measurement and reconstruction of ancestral sequence. All three tools out-perform the leading neutral DNA simulator (DAWG) in benchmarks. The programs are available at .
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spelling pubmed-27608742009-10-13 Tools for simulating evolution of aligned genomic regions with integrated parameter estimation Varadarajan, Avinash Bradley, Robert K Holmes, Ian H Genome Biol Software Controlled simulations of genome evolution are useful for benchmarking tools. However, many simulators lack extensibility and cannot measure parameters directly from data. These issues are addressed by three new open-source programs: GSIMULATOR (for neutrally evolving DNA), SIMGRAM (for generic structured features) and SIMGENOME (for syntenic genome blocks). Each offers algorithms for parameter measurement and reconstruction of ancestral sequence. All three tools out-perform the leading neutral DNA simulator (DAWG) in benchmarks. The programs are available at . BioMed Central 2008 2008-10-08 /pmc/articles/PMC2760874/ /pubmed/18840304 http://dx.doi.org/10.1186/gb-2008-9-10-r147 Text en Copyright © 2008 Varadarajan et al.; 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
Varadarajan, Avinash
Bradley, Robert K
Holmes, Ian H
Tools for simulating evolution of aligned genomic regions with integrated parameter estimation
title Tools for simulating evolution of aligned genomic regions with integrated parameter estimation
title_full Tools for simulating evolution of aligned genomic regions with integrated parameter estimation
title_fullStr Tools for simulating evolution of aligned genomic regions with integrated parameter estimation
title_full_unstemmed Tools for simulating evolution of aligned genomic regions with integrated parameter estimation
title_short Tools for simulating evolution of aligned genomic regions with integrated parameter estimation
title_sort tools for simulating evolution of aligned genomic regions with integrated parameter estimation
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760874/
https://www.ncbi.nlm.nih.gov/pubmed/18840304
http://dx.doi.org/10.1186/gb-2008-9-10-r147
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