Data from: The early spread and epidemic ignition of HIV-1 in human populations

Faria NR, Rambaut A, Suchard MA, Baele G, Bedford T, Ward MJ, Tatem AJ, Sousa JD, Arinaminpathy N, Pépin J, Posada D, Peeters M, Pybus OP, Lemey P

Date Published: October 3, 2014

DOI: http://dx.doi.org/10.5061/dryad.nn952

 

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Title Preliminary Analysis
Downloaded 105 times
Description Contains (1) BEAST XML input file, (2) empirical tree distribution (1,000 trees) (GTR+gamma substitution model, uncorrelated relaxed clock model, skygrid tree prior), and (3) nexus format sequence alignment.
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Title Sequence data details and alignments for data sets A to D
Downloaded 62 times
Description Contains (1) table with accession numbers, isolate names, sampling years, country/location of sampling and (2) nexus format sequence alignments.
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Title Phylogeographic models and empirical tree distributions for data sets A to D
Downloaded 137 times
Description Contains (1) the BEAST XML input file used to generate Figure 1; (2) BEAST XML files used to generate the phylogeographic analyses with an asymmetric diffusion model in Tables S2-S5; and (3) empirical tree distributions (2,000 trees) (GTR+gamma substitution model, uncorrelated relaxed clock model, skygrid tree prior).
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Title Exponential-logistic coalescent model, robust counting and randomisation procedure
Downloaded 72 times
Description Contains (1) the BEAST XML input file for the exponential-logistic coalescent model used to estimate the epidemiological transition time, (2) the BEAST XML input file for the robust counting analysis (Fig. 3 and Figs. S5-S6), and (3) the BEAST XML input file corresponding to the randomisation procedure shown in Fig. S4.
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When using this data, please cite the original publication:

Faria NR, Rambaut A, Suchard MA, Baele G, Bedford T, Ward MJ, Tatem AJ, Sousa JD, Arinaminpathy N, Pépin J, Posada D, Peeters M, Pybus OP, Lemey P (2014) The early spread and epidemic ignition of HIV-1 in human populations. Science 346(6205): 56-61. http://dx.doi.org/10.1126/science.1256739

Additionally, please cite the Dryad data package:

Faria NR, Rambaut A, Suchard MA, Baele G, Bedford T, Ward MJ, Tatem AJ, Sousa JD, Arinaminpathy N, Pépin J, Posada D, Peeters M, Pybus OP, Lemey P (2014) Data from: The early spread and epidemic ignition of HIV-1 in human populations. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.nn952
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