getTree: Create a phylogenetic tree
In Roestlab/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Description Usage Arguments Value Author(s) See Also Examples

Builds a phylogenetic tree from the distance matrix using UPGMA algorithm.

1	getTree(distMat)

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

upgma, getNodeIDs

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)
labels(distMat); length(distMat)
## Not run: 
getTree(distMat)

## End(Not run)
tree <- ape::read.tree(text = "(run1:9,(run2:7,run0:2)master2:5)master1;")
plot(tree, show.node.label = TRUE)