library(ggtree)
phyfile <- system.file("extdata", "sample.phy", package="ggtree")
phylip <- read.phylip(phyfile)
phylip

## 'phylip' S4 object that stored information of
##   '/Users/guangchuangyu/Library/R/3.2/library/ggtree/extdata/sample.phy'.
## 
## ...@ tree: 
## Phylogenetic tree with 15 tips and 13 internal nodes.
## 
## Tip labels:
##  K, N, D, L, J, G, ...
## 
## Unrooted; no branch lengths.
## 
## with sequence alignment available (15 sequences of length 2148)

ggtree(phylip) + geom_tiplab()

msaplot(phylip, offset=1)