Distances walkthrough

First load the libraries you need.

library(ape)
library(phangorn)
library(network)

## network: Classes for Relational Data
## Version 1.12.0 created on 2015-03-04.
## copyright (c) 2005, Carter T. Butts, University of California-Irvine
##                     Mark S. Handcock, University of California -- Los Angeles
##                     David R. Hunter, Penn State University
##                     Martina Morris, University of Washington
##                     Skye Bender-deMoll, University of Washington
##  For citation information, type citation("network").
##  Type help("network-package") to get started.

Load the multiple sequence alignment using read.dna from the ape library.

myalignment.filename <- "ray2000_pruned_degapped.fas"
myalignment <- read.dna(myalignment.filename,format="fasta",as.matrix=TRUE)

Calculate distances using the TN93 model.

myalignment.dist.tn93 <- dist.dna(myalignment,model="TN93",as.matrix=TRUE)

Plot out the distances.

hist(myalignment.dist.tn93[lower.tri(myalignment.dist.tn93)],xlab="Distance",ylab="Frequency",main="",col="grey")

plot of chunk plot_distances
Figure: plot of chunk plot_distances

Calculate a neighbour joining tree.

myalignment.tn93.nj <- nj(myalignment.dist.tn93)

Plot the tree out and add a scale bar.

plot(myalignment.tn93.nj,"unrooted",cex=0.5)
add.scale.bar(length=0.1)

plot of chunk plot_tree
Figure: plot of chunk plot_tree

Bootstrap the alignment; we first define a function to make a tree from the alignment, then call boot.phylo.

maketree <- function(x) nj(dist.dna(x,model="TN93"))
myalignment.tn93.nj.boot <- boot.phylo(myalignment.tn93.nj,myalignment,maketree,B=100,block=3,trees=TRUE,quiet=FALSE,rooted=FALSE)

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## Calculating bootstrap values... done.

Now we can add the bootstrap supports to the tree.

plotBS(myalignment.tn93.nj,myalignment.tn93.nj.boot$trees,type="phylogram",cex=0.5)

plot of chunk plot_bootstrap
Figure: plot of chunk plot_bootstrap

We can also create a network of 'similar' sequences, by defining a threshold distance.

thresh <- 0.01
myalignment.dist.tn93.net <- network(myalignment.dist.tn93<=thresh)
plot(myalignment.dist.tn93.net)

plot of chunk plot_network
Figure: plot of chunk plot_network