BEAST log data from: Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in IAV from North American swine

https://doi.org/10.15482/USDA.ADC/1528285
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posted on 2024-02-21, 17:57 authored by David HufnagelDavid Hufnagel, Katharine M. Young, Zebulun Arendsee, Claire L. Gay, Joaquin Caceres, Daniela S. Rajao, Daniel R. Perez, Amy L. Vincent Baker, Tavis K. Anderson

These are the ".log" files from "Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in Influenza A virus (IAV) from North American swine" generated in BEAST and used to plot molecular substitution rates and calculate statistical distances between posterior distributions of these rates. The names of these files communicate information about the various BEAST runs using the following format: cladeOrLineageName_replicate_substitutionModel_treePrior_MCMCiterations_dateOfRunWithin2021.log where replicate is not always included <div> Resources in this dataset:</div> <ul><li>Resource Title: BEAST log file for clade N1.C.2.1. File Name: N1C21_SRD06_strict_GMRF_200MNov9.log.zipResource Software Recommended: Tracer v1.7.1,url: <a href="http://tree.bio.ed.ac.uk/software/tracer/">http://tree.bio.ed.ac.uk/software/tracer/</a> </li> <li>Resource Title: BEAST log file for clade N1.C.2. File Name: N1C2_SRD06_strict_GMRF_200MNov2.log.zipResource Software Recommended: Tracer v1.7.1,url: <a href="http://tree.bio.ed.ac.uk/software/tracer/">http://tree.bio.ed.ac.uk/software/tracer/</a> </li> <li>Resource Title: BEAST log file for clade N1.C.3.1. File Name: N1C31_SRD06_strict_GMRF200M.log.zipResource Software Recommended: Tracer v1.7.1,url: <a href="http://tree.bio.ed.ac.uk/software/tracer/">http://tree.bio.ed.ac.uk/software/tracer/</a> </li> <li>Resource Title: BEAST log file for clade N1.C.3.2. File Name: N1C32_SRD09_strict_GMRF_200MMay21.log.zipResource Software Recommended: Tracer v1.7.1,url: <a href="http://tree.bio.ed.ac.uk/software/tracer/">http://tree.bio.ed.ac.uk/software/tracer/</a> </li> <li>Resource Title: BEAST log file for clade N1.C.3. File Name: N1C3_r1_hkyGamma4_GMRF_200MMay20.log.zipResource Software Recommended: Tracer v1.7.1,url: <a href="http://tree.bio.ed.ac.uk/software/tracer/">http://tree.bio.ed.ac.uk/software/tracer/</a> </li> <li>Resource Title: BEAST log file for clade N1.P. File Name: N1P_SRD06_strict_GMRF_200MAug2.log.zipResource Software Recommended: Tracer v1.7.1,url: <a href="http://tree.bio.ed.ac.uk/software/tracer/">http://tree.bio.ed.ac.uk/software/tracer/</a> </li> <li>Resource Title: BEAST log file for the classical swine N1 lineage. File Name: N1classical_r1_SRD06_UCLN_GMRF_200MMay21.log.zipResource Software Recommended: Tracer v1.7.1,url: <a href="http://tree.bio.ed.ac.uk/software/tracer/">http://tree.bio.ed.ac.uk/software/tracer/</a> </li></ul>

Funding

USDA-ARS: 5030-32000-23 1-000-D

USDA-ARS: 5030-32000-231-025-S

National Institute of Allergy and Infectious Diseases: 75N93021C00015

National Institute of Allergy and Infectious Diseases: 75N93021C00014

Oak Ridge Institute for Science and Education: DE-AC05-06OR23100

Defense Advanced Research Projects Agency: HR00112020034

USDA-ARS: 0500-00093-001-00-D

History

Related Materials

1.
DOI - Is supplement to Hufnagel, D. E., Young, K. M., Arendsee, Z. W., Gay, L. C., Caceres, C. J., Rajão, D. S., Perez, D. R., Vincent Baker, A. L., & Anderson, T. K. (2023). Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in influenza A virus from North American swine. Virus Evolution, 9(1). https://doi.org/10.1093/ve/vead015

Data contact name

Anderson, Tavis

Data contact email

tavis.anderson@usda.gov

Publisher

Ag Data Commons

Intended use

The primary use is for replication of results, but this data could also be used to compare molecular substitution rates or other BEAST-generated statistics to other's data

Temporal Extent Start Date

1930-01-01

Temporal Extent End Date

2020-09-03

Theme

Not specified

Geographic Coverage

Geographic location - description

USA+Canada+Mexico+CostaRica+Guatemala+Cuba

ISO Topic Category

biota
farming
health

National Agricultural Library Thesaurus terms

genetic variation; antigenic variation; sialidase; swine; Bayesian theory; Influenza A virus; phylogeny; molecular genetics; North America

OMB Bureau Code

005:18 - Agricultural Research Service

OMB Program Code

005:040 - National Research

ARS National Program Number

Pending citation

Public Access Level

Public

Preferred dataset citation

Hufnagel, David E.; Young, Katharine M.; Arendsee, Zebulun; Gay, Claire L.; Caceres, Joaquin; Rajao, Daniela S.; Perez, Daniel R.; Vincent Baker, Amy L.; Anderson, Tavis K. (2022). BEAST log data from: Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in IAV from North American swine. Ag Data Commons. https://doi.org/10.15482/USDA.ADC/1528285

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Keywords

BEAST molecular substitution rate rate of evolution Bayesian statistics Influenza A virus Swine neuraminidase evolution phylogenetic NP103 data.gov ARS

Licence

U.S. Public Domain