My code in R is:

stage 1

x <- read.alignment("humanSeqAligned.fasta", format= "fasta")

stage 2

cleanx <- cleanAlignment(x, 30, 30)

stage3

dBin<-as.DNAbin(cleanx)

stage4

dist <- dist.dna(dBin, model = "K80", variance = FALSE, gamma = FALSE, pairwise.deletion = FALSE, base.freq = NULL, as.matrix = FALSE)

stage5

neighbor <- nj(dist)

stage6

humanSeqTreeRooted <-root(neighbor, "NC_001643.1", r=TRUE)

stage7

pdf(file='/work/projects/project3/project3tree.pdf', height=8, width=8)

plot.phylo(humanSeqTreeRooted, type='p')

dev.off()

stage 8

s <- prcomp(dist, center=TRUE, scale=TRUE)

stage9

pdf(file='/work/07950/projects/project3/project3pca.pdf', height=8, width=8)

biplot(s)

dev.off()