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

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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


Resources in this dataset:

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

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

{"type":"FeatureCollection","features":[{"geometry":{"type":"Polygon","coordinates":[[[-82.345745265484,9.8327239064169],[-83.164076507092,7.7402148611428],[-85.836760997772,9.4173793620844],[-86.289413273335,11.018860560027],[-85.411022007465,11.154495319768],[-83.253780305386,11.031850314318],[-82.345745265484,9.8327239064169]]]},"type":"Feature","properties":{}},{"geometry":{"type":"Polygon","coordinates":[[[-90.357213914394,13.571259814305],[-89.156501591206,14.593867742357],[-88.118993639946,15.922493702258],[-79.930405318737,21.028753398843],[-77.613800168037,19.434517765207],[-73.612276911736,20.117839630492],[-81.027136445045,23.90774637848],[-79.595024585724,27.116179878336],[-50.640728473663,47.361000390678],[-74.956884384155,75.555035919386],[-58.406581878662,82.637318822619],[-76.563377380371,84.115459571006],[-170.49639701843,71.975163797827],[-174.56365585327,55.62964345413],[-125.10432243347,32.51272930836],[-105.14683127403,18.209275138895],[-90.357213914394,13.571259814305]]]},"type":"Feature","properties":{}}]}

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

  • 103

Pending citation

  • No

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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    Categories

    Keywords

    BEASTmolecular substitution raterate of evolutionBayesian statisticsInfluenza A virusSwineneuraminidaseevolutionphylogeneticNP103data.govARS

    Licence

    U.S. Public Domain

    Exports

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