![enter image description here][1]

[1]: /media/images/a2487cf2-4f63-4e1b-ac2f-27f81fe2

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()



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