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BEASTling: A software tool for linguistic phylogenetics using BEAST 2

We present a new open source software tool called BEASTling, designed to simplify the preparation of Bayesian phylogenetic analyses of linguistic data using the BEAST 2 platform. BEASTling transforms comparatively short and human-readable configuration files into the XML files used by BEAST to speci...

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Detalles Bibliográficos
Autores principales: Maurits, Luke, Forkel, Robert, Kaiping, Gereon A., Atkinson, Quentin D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5552126/
https://www.ncbi.nlm.nih.gov/pubmed/28796784
http://dx.doi.org/10.1371/journal.pone.0180908
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author Maurits, Luke
Forkel, Robert
Kaiping, Gereon A.
Atkinson, Quentin D.
author_facet Maurits, Luke
Forkel, Robert
Kaiping, Gereon A.
Atkinson, Quentin D.
author_sort Maurits, Luke
collection PubMed
description We present a new open source software tool called BEASTling, designed to simplify the preparation of Bayesian phylogenetic analyses of linguistic data using the BEAST 2 platform. BEASTling transforms comparatively short and human-readable configuration files into the XML files used by BEAST to specify analyses. By taking advantage of Creative Commons-licensed data from the Glottolog language catalog, BEASTling allows the user to conveniently filter datasets using names for recognised language families, to impose monophyly constraints so that inferred language trees are backward compatible with Glottolog classifications, or to assign geographic location data to languages for phylogeographic analyses. Support for the emerging cross-linguistic linked data format (CLDF) permits easy incorporation of data published in cross-linguistic linked databases into analyses. BEASTling is intended to make the power of Bayesian analysis more accessible to historical linguists without strong programming backgrounds, in the hopes of encouraging communication and collaboration between those developing computational models of language evolution (who are typically not linguists) and relevant domain experts.
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spelling pubmed-55521262017-08-25 BEASTling: A software tool for linguistic phylogenetics using BEAST 2 Maurits, Luke Forkel, Robert Kaiping, Gereon A. Atkinson, Quentin D. PLoS One Research Article We present a new open source software tool called BEASTling, designed to simplify the preparation of Bayesian phylogenetic analyses of linguistic data using the BEAST 2 platform. BEASTling transforms comparatively short and human-readable configuration files into the XML files used by BEAST to specify analyses. By taking advantage of Creative Commons-licensed data from the Glottolog language catalog, BEASTling allows the user to conveniently filter datasets using names for recognised language families, to impose monophyly constraints so that inferred language trees are backward compatible with Glottolog classifications, or to assign geographic location data to languages for phylogeographic analyses. Support for the emerging cross-linguistic linked data format (CLDF) permits easy incorporation of data published in cross-linguistic linked databases into analyses. BEASTling is intended to make the power of Bayesian analysis more accessible to historical linguists without strong programming backgrounds, in the hopes of encouraging communication and collaboration between those developing computational models of language evolution (who are typically not linguists) and relevant domain experts. Public Library of Science 2017-08-10 /pmc/articles/PMC5552126/ /pubmed/28796784 http://dx.doi.org/10.1371/journal.pone.0180908 Text en © 2017 Maurits et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Maurits, Luke
Forkel, Robert
Kaiping, Gereon A.
Atkinson, Quentin D.
BEASTling: A software tool for linguistic phylogenetics using BEAST 2
title BEASTling: A software tool for linguistic phylogenetics using BEAST 2
title_full BEASTling: A software tool for linguistic phylogenetics using BEAST 2
title_fullStr BEASTling: A software tool for linguistic phylogenetics using BEAST 2
title_full_unstemmed BEASTling: A software tool for linguistic phylogenetics using BEAST 2
title_short BEASTling: A software tool for linguistic phylogenetics using BEAST 2
title_sort beastling: a software tool for linguistic phylogenetics using beast 2
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5552126/
https://www.ncbi.nlm.nih.gov/pubmed/28796784
http://dx.doi.org/10.1371/journal.pone.0180908
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