Make trees in R

• phangorn package

  data:
          chimp    human1    human2    rhesus
  1   256840694 247285839 247285839 240226291
  2    45217564  43683607  43683607  45916995
  3    64398220  62686694  62686694  59634838
  4     1411042   1378486   1378486   1349406
  5    17502943  16721703  16721703  18163003
  

# 1. distance
d <- dist(t(data))

# 2. plot
# 2.1 hclust
tree <- hclust(d)
plot(tree)

# 2.2 nj and upgma trees
library(phangorn)
# nj tree
tree <- nj(d)
plot(tree,main="nj tree")
plot(tree,'u',main='nj tree')
# upgma tree
tree = upgma(d)
plot(tree,main="upgma tree")