getTree {DIAlignR} | R Documentation |
Builds a phylogenetic tree from the distance matrix using UPGMA algorithm.
getTree(distMat, method = "average")
distMat |
(dist) a pairwise distance matrix. |
(phylo) a tree.
Shubham Gupta, shubh.gupta@mail.utoronto.ca
ORCID: 0000-0003-3500-8152
License: (c) Author (2020) + GPL-3 Date: 2020-05-31
m <- matrix(c(0,1,2,3, 1,0,1.5,1.5, 2,1.5,0,1, 3,1.5,1,0), byrow = TRUE, ncol = 4, dimnames = list(c("run1", "run2", "run3", "run4"), c("run1", "run2", "run3", "run4"))) distMat <- as.dist(m, diag = FALSE, upper = FALSE) ## Not run: tree <- getTree(distMat) ## End(Not run) tree <- ape::read.tree(text = "(run1:9,(run2:7,run0:2)master2:5)master1;") plot(tree, type = "phylogram", show.node.label = TRUE) ape::axisPhylo(1) plot(tree, type = "unrooted", show.node.label = TRUE) ape::edgelabels(tree$edge.length) tree <- ape::nj(distMat) # Neighbor-Joining tree plot(tree, type = "unrooted", show.node.label = TRUE) ape::edgelabels(tree$edge.length)