Minimum Evolution
This short example describes how to use Treeline to optimize balanced minimum evolution (ME) trees. The ME optimality criterion is fast, model based, statistically consistent, and accurate on empirical benchmarks. These features make it the default go-to tree building method in Treeline.How do I build a minimum evolution phylogenetic tree?
First it is necessary to install DECIPHER and load the library in R. Next, convert a sequence alignment into the distance matrix that will be used to optimize the tree.12-3456-789-1011121314-1516171819-2021# load the DECIPHER library in Rlibrary(DECIPHER) # load the target sequences from a filefas <- "<<REPLACE WITH PATH TO FASTA FILE>>"seqs <- readDNAStringSet(fas) # use AA, DNA, or RNAseqs # align coding sequencesseqs <- AlignTranslation(seqs,type="DNAStringSet") # choose AA or DNA # construct a distance matrixD <- DistanceMatrix(seqs,corr="F81+F", # choose a modeltype="dist",processors=NULL) # use all CPUs # optimize the treetree <- Treeline(myDistMatrix=D,method="ME",showPlot=TRUE,processors=NULL) # use all CPUs # optionally, output a Newick fileWriteDendrogram(tree, file="")