library(phangorn)

accessionNumbers <- c("U15717", "U15718", "U15719", "U15720", "U15721", "U15722", "U15723", "U15724") #These come from a paper by Paradis (1997) on Tanagers

#USE THE read.GenBank command TO DOWNLOAD THESE SEQUENCES FROM GENBANK AND PUT THEM IN AN OBJECT CALLED sequences.
sequences<-read.GenBank(accessionNumbers)
#Note that it's read.GenBank, not read.Genbank, read.genbank, readGenBank, etc. Programming is usually very case-sensitive

distanceMatrix<-dist.dna(sequences) #get a distance matrix
print(distanceMatrix)
convertedSeqs<-phyDat(sequences) #convert to a format useful for phangorn

treeBad<-upgma(distanceMatrix)
#the UPGMA starting tree actually is not that bad (and a NJ tree is the same as the maximum parsimony tree). So let's make it challenging by giving you a bad starting tree (for larger problems, you would not have this "problem" of a starting tree that is too good)
while(parsimony(treeBad,convertedSeqs)<220) {
		treeBad<-rNNI(treeBad)	
}

maximumTries<-50

#GET SCORE OF STARTING TREE, treeBad
#STORE THE CURRENT BEST TREE, WHICH IS treeBad

#PRINT THE STARTING SCORE

for (tryNumber in 1:maximumTries) {
	#GET A NEW TREE BY DOING newTree<-rNNI(  __SOMETHING__ ) 
	#COMPARE THE SCORE OF THE NEW TREE TO THE OLD TREE
	#USE AN IF BLOCK (if (new<old) { THINGS TO DO } ) TO DO SOMETHING IF THE NEW TREE IS BETTER
	#INFO ON IF() IS AT http://cran.r-project.org/doc/manuals/R-intro.html#Conditional-execution
	#HERE IS AN EXAMPLE BLOCK
	if (1<2) {
		print("one is less than 2")	
	}
	#PERHAPS MORE THINGS AFTER THE IF BLOCK
}

#PRINT THE FINAL SCORE

#PLOT THE FINAL TREE

#BONUS: THINK OF A WAY TO DO AN EXHAUSTIVE SEARCH USING THE allTrees COMMAND. WILL THIS WORK FOR MANY MORE TAXA?