Data from: Measuring asymmetry in time-stamped phylogenies

Dearlove BL, Frost SDW

Date Published: August 11, 2015

DOI: http://dx.doi.org/10.5061/dryad.v7817

 

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Title Trees in newick format
Downloaded 71 times
Description This is a .zip file containing the within-host HIV, H5N1 influenza and ebola virus trees in Newick format which were analysed in the paper. Many thanks to Andrew Rambaut (University of Edinburgh) for providing the ebola phylogeny. Data originally from: 1) Within-host HIV (P83_HIV.nwk) Frost SDW, Wrin T, Smith DM, Kosakovsky Pond SL, Liu Y, et al. (2005) Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection. Proc Natl Acad Sci USA 102: 18514-9 2) H5N1 influenza (H5N1_flu.nwk) Wallace RG, HoDac H, Lathrop RH, Fitch WM (2007) A statistical phylogeography of influenza A H5N1. Proc Natl Acad Sci USA 104: 4473-4478. 3) Ebola Virus (Ebola.nwk) Gire SK, Goba A, Andersen KG, Sealfon RSG, Park DJ, et al. (2014) Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 345: 1369-1372.
Download Trees.zip (8.172 Kb)
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Title treeImbalance
Downloaded 4 times
Description An R package containing the functions used for detecting asymmetry as described in the paper.
Download treeImbalance_1.1.tar.gz (6.924 Kb)
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Title R script for analysis of trees
Downloaded 13 times
Description R script used in the analysis of the HIV, influenza and ebola trees, and to produce figures 4, 6 and 7. Requires the ape, cluster, phylobase and adephylo packages in addition to the treeImbalance package included in this repository.
Download example-analysis-script.R (8.451 Kb)
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When using this data, please cite the original publication:

Dearlove BL, Frost SDW (2015) Measuring asymmetry in time-stamped phylogenies. PLOS Computational Biology 11(7): e1004312. http://dx.doi.org/10.1371/journal.pcbi.1004312

Additionally, please cite the Dryad data package:

Dearlove BL, Frost SDW (2015) Data from: Measuring asymmetry in time-stamped phylogenies. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.v7817
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