Introduction to phylogenetics using R

This practical provides an overview of different phylogenetic reconstruction methods in R, using influenza virus sequences.

Click on the tree to access the pdf:

Content of the repository

This repository contains the following files:

• phylo-practical.Rnw: the knitr document of the practical
• phylo-practical.pdf: the pdf version of the practical; to recompile it freshly, use: knitr::knit2pdf("phylo-practical.Rnw")
• data/: a folder containing two datasets:
  • usflu.annot.csv: annotations of the sequences
  • usflu.fasta: a fasta file containing aligned sequences
• figs/: figures produced by knitr as well as images used to generate the pdf

Compiling this document yourself

To compile this document, you first need to download a handful of files:

## file URLs
base.url <- "https://raw.githubusercontent.com/reconhub/phylo-practical/master/"
files.to.get <- c("phylo-practical.Rnw", "biblioTJ.bib", "Rlogo.pdf", "ygg.jpg")
urls <- paste0(base.url, files.to.get)

## set working directory - change 'dest.dir' as you want
dest.dir <- "phylo-practical"
if (!dir.exists(dest.dir)) dir.create(dest.dir)
setwd(dest.dir)
dir.create("figs")

## download files
for (i in seq_along(urls)) {
  download.file(urls[[i]], files.to.get[i], method = "curl")
}

And then compile the document using:

knitr::knit2pdf("phylo-practical.Rnw")

Feedback & contributions

Please send feedback using the issues system. Contributions are welcome as pull requests.

Credits

Author: Thibaut Jombart

Licence: this work is released under Creative Common Attribution 4.0.