### ML Sequence-structure tree calculation

To install the phangorn package, type:
```	install.packages("phangorn")

```

#### 2 Calculate the sequence-structure tree based on maximum likelihood

In this examples we use a one-letter coded .fasta file containing sequence and structure information.
```	# Load the phangorn librariy
library(phangorn)

# Read the aligned .fasta file (one letter encoded sequence and structure)
file = "c:/path_to/seq_str_one_letter_code.fasta"

# Calculate the maximum likelihood tree
dm   = dist.ml(dat)
tree = NJ(dm)

# estimate a GTR+I+G ML tree using the nj tree as starting tree
fitStart = pml(tree, dat, k=4, inv=.2)
fit = optim.pml(fitStart, TRUE, TRUE, TRUE, TRUE, TRUE,TRUE)

# plot tree
root_name = "NameOfSpeciesWithinDataset"
type="phylogram", show.node.label=T,underscore=T,cex=0.8,no.margin=T)

# plot bootstraped tree
bs  = bootstrap.pml(fit, bs=100, optNni=TRUE)
treeBS = plotBS(fit\$tree, bs, type="phylogram", bs.col="red", bs.adj=NULL)

# save ML tree
write.tree(fit\$tree,file="ML_GTR_I_G.tre")

# save ML Bootstrap tree
write.tree(treeBS,file="BS_ML_GTR_I_G.tre")
```

#### References:

R Core Team (2014) R: A Language and Environment for Statistical Computing. http://www.R-project.org

Schliep K.P. (2011) phangorn: phylogenetics analysis in R. Bioinformatics, 15;27(4):592-3

Wolf, M., Koetschan, C., Müller, T. (2014) ITS2, 18S, 16S or any other RNA — simply aligning sequences and their individual secondary structures simultaneously by an automatic approach. Gene, 546(2):145-9