zika.2015: Zika virus, 2015-2016

In Hackout3/timetrees: A Collection of Time-Stamped Phylogenies

Description

These data comprise of a tree, metadata, and a multiple sequence alignment of Zika virus, sampled from 15 different countries since 2015.

Usage

zika.2015

Format

A list with three elements

tree

A phylogeny as a phylo object

data

Metadata as a data frame with 58 rows and 6 columns

aln

Multiple sequence alignment, as a DNAbin object, stored as a matrix

Author(s)

Data from the Zika version of nextstrain.org by Trevor Bedford and Richard Neher, compiled from multiple sources, as listed on the webpage. Transfer to R and documentation by Simon Frost ([e-mail]).

Source

http://nextstrain.org/zika

References

Neher RA, Bedford T. 2015. nextflu: real-time tracking of seasonal influenza virus evolution in humans. Bioinformatics 10.1093/bioinformatics/btv381.

Examples

library(ape)
## show metadata for first few sequences
head(zika.2015$data)
## plot tree
plot(zika.2015$tree)
## summarise sequence data
zika.2015$aln

Hackout3/timetrees documentation built on May 6, 2019, 10:53 p.m.