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---
title: "Phylogenetic Biology"
author: "Casey W. Dunn"
github-repo: caseywdunn/phylogenetic_biology
twitter-handle: caseywdunn
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
documentclass: book
bibliography: [book.bib, packages.bib]
biblio-style: apalike
link-citations: yes
description: "An introduction to Phylogenetic Biology."
fig_caption: yes
---
```{r preliminaries, include=FALSE}
# The following should be installed from github with the specified
# devtools command. You will need to install devtools first.
library( treeio ) # devtools::install_github("GuangchuangYu/treeio")
library( ggtree ) # devtools::install_github("GuangchuangYu/ggtree")
library( ape )
library( geiger )
library( gridExtra )
library( magrittr )
library( phytools )
library( stringr )
library( tidyverse )
library( Matrix )
source( "functions.R" )
set.seed( 23456 )
```
```{r setup, include=FALSE}
knitr::opts_chunk$set(
message = FALSE,
warning = FALSE,
echo = FALSE,
dpi = 300,
cache = FALSE
)
```
```{r include=FALSE}
# automatically create a bib database for R packages
knitr::write_bib(c(
.packages(), 'bookdown', 'knitr', 'rmarkdown', 'ape', 'geiger', 'ggtree', 'treeio', 'phytools'
), 'packages.bib')
```
# Preface {-}
I developed this book as a collection of the concepts, methods, and applications that I most wanted to share with students in my Phylogenetic Biology courses. It is really my lecture notes dessed up in the form of the rough draft of a book.
## Source code
The source code for this manuscript is available on [github]( https://github.com/caseywdunn/phylogenetic_biology). The book was rendered from the source with `bookdown` [@bookdown2016].
Please submit any errors you find, typos, or suggestions that you have for improving the manuscript to the [issue tracker](https://github.com/caseywdunn/phylogenetic_biology/issues).
## Other resources
The following sites have a wide variety of material that is relevant to the
theory and and practice of phylogenetic biology.
- An extensive list of tools, tutorials, and examples of phylogenetic tools in
the programming language R maintained by Briam O'Meara:
[CRAN Task View: Phylogenetics](https://cran.r-project.org/web/views/Phylogenetics.html)
- The Workshop on Molecular Evolution at Woods Hole. This is an intensive summer
course on phylogenetics, with an emphasis on building phylogenetic trees. Check
out the faculty pages for lecture pdfs:
[Workshop on Molecular Evolution](https://molevolworkshop.github.io)
- The Applied Phylogenetics Workshop in Bodega Bay. This is another summer course
on phylogenetics, but with a bit more emphasis on using phylogenies to test
evolutionary questions:
[Applied Phylogenetics Workshop](http://treethinkers.org/tutorials/)
The following books are great resources for learning more about phylogenetic biology:
- Baum, D. and Smith, S. (2012). Tree Thinking. An Introduction to Phylogenetic
Biology. [Roberts Publishers](http://www.roberts-publishers.com/tree-thinking-an-introduction-to-phylogenetic-biology.html).
- Paradis, E. (2011) Analysis of Phylogenetics and Evolution with R.
[Springer](http://www.springer.com/life+sciences/evolutionary+%26+developmental+biology/book/978-0-387-32914-7)
- Felsenstein, J. (2004) Inferring phylogenies.
[Sinauer Associates](http://www.sinauer.com/detail.php?id=1775).
- Swofford, D. L., Olsen, G. J., Waddell, P. J., & Hillis, D. M. (1996).
Phylogenetic inference. In: Molecular Systematics, Second Edition. eds: D. M.
Hillis, C Moritz, & B. K. Mable. [Sinauer Associates](http://www.sinauer.com/detail.php?id=1775)
The following books provide general computational background for the topics covered here:
- Wickham, H., Grolemund, G (2017) R for Data Science. https://r4ds.had.co.nz
- Haddock, S. H. D. and Dunn, C. W. (2010). Practical Computing for Biologists. http://practicalcomputing.org
## Software versions
This book was rendered from the source code on `r format( Sys.time(), "%a %b %d %X %Y" )` with the following R package versions.
```{r session_summary, echo=FALSE, comment=NA}
sessionInfo()
```
## License
This manuscript is distrubuted under a [Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License]( https://creativecommons.org/licenses/by-nc-nd/3.0/us/).