Data from: A synchronized global sweep of the internal genes of modern avian influenza virus

Worobey M, Han G, Rambaut A

Date Published: February 17, 2014

DOI: http://dx.doi.org/10.5061/dryad.m04j9

 

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Title Figure 1 GTR.zip
Downloaded 157 times
Description Contains (1) the nexus format sequence alignments, (2) the BEAST XML input files for the HSLC analyses (GTR+gamma substitution model), (3) the maximum clade credibility (MCC) tree files, and (4) a PDF of the full tree figures corresponding to the 8 panels in Figure 1.
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Title Figure 1 3rd sites.zip
Downloaded 64 times
Description Contains (1) the nexus format sequence alignments, (2) the BEAST XML input files for the HSLC analyses, and (3) the maximum clade credibility (MCC) tree files for the analysis of 3rd codon position sites of the Figure 1 data sets.
Download Figure 1, 3rd sites.zip (1.045 Mb)
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Title Figure 1, SRD.zip
Downloaded 91 times
Description Contains (1) the BEAST XML input files for the HSLC analyses of the Figure 1 data under the SRD06 substitution model and (2) the resulting maximum clade credibility (MCC) tree files. The alignments used are the same as those in Figure 1 GTR.zip.
Download Figure 1, SRD.zip (2.008 Mb)
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Title Figure 1, subsampled.zip
Downloaded 59 times
Description Contains (1) the nexus format sequence alignments, (2) the BEAST XML input files for the HSLC analyses, and (3) the maximum clade credibility (MCC) tree files for H3 and N8 data sets. The “stemfalse” files assume that the stem branch of the equine H3N8 clade evolved at the avian substitution rate, while the other files assume this branch evolved at the equine rate.
Download Figure 1, subsampled.zip (686.4 Kb)
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Title UCLD relaxed clock.zip
Downloaded 78 times
Description Contains (1) the BEAST XML input files for the UCLD relaxed clock analyses (SRD06 substitution model), and (2) the resulting maximum clade credibility (MCC) tree files. The alignments used are the same as those in Figure 1 GTR.zip.
Download UCLD relaxed clock.zip (1.652 Mb)
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Title Randomly sampled sequences.zip
Downloaded 61 times
Description Contains (1) the nexus format sequence alignments, (2) the BEAST XML input files for the HSLC analyses (SRD06 substitution model), and (3) the maximum clade credibility (MCC) tree files for alignments of randomly sampled sequences (created independently of the Figure 1 data sets).
Download randomly sampled sequences.zip (895.3 Kb)
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Title Figure 1 data plus new sequences.zip
Downloaded 74 times
Description These files are based on the Figure 1 data sets with the addition of the three newly sequenced complete genomes from this study (A/chicken/Japan/1925, A/duck/Manitoba/1953, and A/equine/Detroit/3/1964). For PB1, several sequences from South America were also added. Contains (1) the nexus format sequence alignments, (2) the BEAST XML input files for the HSLC analyses (SRD06 substitution model), (3) the maximum clade credibility (MCC) tree files, and (4) a PDF of the full tree figures corresponding to the 8 panels in Figure 1 (except with the additional sequences and using the SRD06 substitution model).
Download Figure 1 data plus new sequences.zip (1.269 Mb)
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Title H3 and N8.zip
Downloaded 61 times
Description Contains (1) the nexus format sequence alignments, (2) the BEAST XML input files for the HSLC analyses, and (3) the maximum clade credibility (MCC) tree files for H3 and N8 data sets. The “stemfalse” files assume that the stem branch of the equine H3N8 clade evolved at the avian substitution rate, while the other files assume this branch evolved at the equine rate.
Download H3 and N8.zip (481.2 Kb)
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Title Figure3.zip
Downloaded 75 times
Description Contains (1) the nexus format sequence alignments, (2) the BEAST XML input files and (3) the resulting maximum clade credibility (MCC) tree files for the HA and NA diversity analyses reported in Figure 3.
Download Figure 3.zip (778.0 Kb)
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Title Giant Alignment.zip
Downloaded 109 times
Description Contains the FASTA format sequence alignments for the IAV sequence data preparation.
Download Giant Alignment.zip (6.921 Mb)
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When using this data, please cite the original publication:

Worobey M, Han G, Rambaut A (2014) A synchronized global sweep of the internal genes of modern avian influenza virus. Nature 508(7495): 254–257. http://dx.doi.org/10.1038/nature13016

Additionally, please cite the Dryad data package:

Worobey M, Han G, Rambaut A (2014) Data from: A synchronized global sweep of the internal genes of modern avian influenza virus. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.m04j9
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