ML Sequence-structure tree calculation

1 Download and install R including the phangorn package

Download the lastest R-version from www.r-project.org.
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"
	dat  = read.phyDat(file,format="fasta", type="AA")

	# 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"
	plot(ladderize(root(fit$tree, match(root_name,fit$tree$tip.label))),
		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