MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R
SUMMARY: MSCquartets is an R package for species tree hypothesis testing, inference of species trees and inference of species networks under the Multispecies Coalescent model of incomplete lineage sorting and its network analog. Input for these analyses are collections of metric or topological locus...
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ftpubmed:oai:pubmedcentral.nih.gov:8289379 2023-05-15T17:14:03+02:00 MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R Rhodes, John A Baños, Hector Mitchell, Jonathan D Allman, Elizabeth S 2020-10-08 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8289379/ http://www.ncbi.nlm.nih.gov/pubmed/33031510 https://doi.org/10.1093/bioinformatics/btaa868 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8289379/ http://www.ncbi.nlm.nih.gov/pubmed/33031510 http://dx.doi.org/10.1093/bioinformatics/btaa868 © The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_modelThis article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model) Bioinformatics Applications Notes Text 2020 ftpubmed https://doi.org/10.1093/bioinformatics/btaa868 2021-10-10T00:22:43Z SUMMARY: MSCquartets is an R package for species tree hypothesis testing, inference of species trees and inference of species networks under the Multispecies Coalescent model of incomplete lineage sorting and its network analog. Input for these analyses are collections of metric or topological locus trees which are then summarized by the quartets displayed on them. Results of hypothesis tests at user-supplied levels are displayed in a simplex plot by color-coded points. The package implements the QDC and WQDC algorithms for topological and metric species tree inference, and the NANUQ algorithm for level-1 topological species network inference, all of which give statistically consistent estimators under the model. AVAILABILITY AND IMPLEMENTATION: MSCquartets is available through the Comprehensive R Archive Network: https://CRAN.R-project.org/package=MSCquartets. Text nanuq PubMed Central (PMC) Bioinformatics 37 12 1766 1768 |
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Applications Notes Rhodes, John A Baños, Hector Mitchell, Jonathan D Allman, Elizabeth S MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R |
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Applications Notes |
description |
SUMMARY: MSCquartets is an R package for species tree hypothesis testing, inference of species trees and inference of species networks under the Multispecies Coalescent model of incomplete lineage sorting and its network analog. Input for these analyses are collections of metric or topological locus trees which are then summarized by the quartets displayed on them. Results of hypothesis tests at user-supplied levels are displayed in a simplex plot by color-coded points. The package implements the QDC and WQDC algorithms for topological and metric species tree inference, and the NANUQ algorithm for level-1 topological species network inference, all of which give statistically consistent estimators under the model. AVAILABILITY AND IMPLEMENTATION: MSCquartets is available through the Comprehensive R Archive Network: https://CRAN.R-project.org/package=MSCquartets. |
format |
Text |
author |
Rhodes, John A Baños, Hector Mitchell, Jonathan D Allman, Elizabeth S |
author_facet |
Rhodes, John A Baños, Hector Mitchell, Jonathan D Allman, Elizabeth S |
author_sort |
Rhodes, John A |
title |
MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R |
title_short |
MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R |
title_full |
MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R |
title_fullStr |
MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R |
title_full_unstemmed |
MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R |
title_sort |
mscquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in r |
publisher |
Oxford University Press |
publishDate |
2020 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8289379/ http://www.ncbi.nlm.nih.gov/pubmed/33031510 https://doi.org/10.1093/bioinformatics/btaa868 |
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nanuq |
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nanuq |
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Bioinformatics |
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8289379/ http://www.ncbi.nlm.nih.gov/pubmed/33031510 http://dx.doi.org/10.1093/bioinformatics/btaa868 |
op_rights |
© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_modelThis article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model) |
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https://doi.org/10.1093/bioinformatics/btaa868 |
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Bioinformatics |
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12 |
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1766 |
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1768 |
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1766071306335289344 |