About this Book
- Skills Level
- AnVIL Collection
BOOK OVERVIEW
1 Introduction
BEFORE YOU START
2 Sign in
3 Create a workspace
RUNNING RSTUDIO
4 Working in RStudio
TREE THINKING
5 Phylogenetics basics
6 Visualizing trees in R
GETTING SEQUENCES
7 What sequences should I choose?
8 Finding sequences in GenBank
9 Downloading the sequences from GenBank
- 9.1 The DNA.bin object
- 9.2 The fasta format
ALIGNMENT
10 Why do we align sequences?
11 Creating a multiple sequence alignment
NEIGHBOR JOINING
12 The neighbor joining method of tree estimation
- 12.1 Models of molecular evolution
13 Building a neighbor joining tree
PARSIMONY
14 The parsimony method of tree estimation
- 14.1 Parsimony
- 14.2 Tree searching methods
15 Building a parsimony tree
MORE TREE THINKING
16 More Phylogenetics Basics
MAXIMUM LIKELIHOOD
17 What is Maximum Likelihood?
18 Estimating a tree using Maximum Likelihood
TIME TREES
19 What is a time tree?
- 19.1 Molecular clocks
- 19.2 Calibration points
20 Adding calibration points to your phylogenies
PHYLOGENETIC NETWORKS
21 What is a network?
- 21.1 Why do we see competing phylogenetic relationships?
22 Visualizing phylogenetic networks
- 22.1 Using DensiTree
- 22.2 Networks in R
ANCESTRAL STATE RECONSTRUCTION
23 Ancestral state reconstruction
About the Authors
24 References

Molecular Phylogenetic Techniques

Chapter 24 References

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All other materials CC-BY unless noted otherwise.