reading and manipulating phylogenies in R

#Pacakges
require(picante)

#reading nexus files:
my.phylo=read.nexus(file.choose())

# Consensus tree
arvore.cons=consensus(my.phylo,p=1, check.labels=T)

#Ultrametricize tree:
ultra.tree=compute.brlen(arvore.cons, method = "Grafen", power = 1) 

# Save as "tre":
write.tree(ultra.tree,"phylogeny")

# Opening the new "phylogeny" file
cons=read.tree(file.choose())

# Visualization
plot(cons, cex=0.5)

# Checking values
summary(cons)
# or
cons

# Check the terminal node names
list1<- (cons$tip.label)
list1

# Exporting names:
write.csv(list1, file = "list.csv")

# Inserting scale bar
#add.scale.bar(cons, lenght = 0.1)