getTree {DIAlignR} | R Documentation

## Create a phylogenetic tree

### Description

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

### Usage

    getTree(distMat, method = "average")

### Arguments

`distMat` | (dist) a pairwise distance matrix.

### Value

(phylo) a tree.

### Author(s)

Shubham Gupta, shubh.gupta@mail.utoronto.ca

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2020-05-31

### See Also

`upgma, getNodeIDs`

### Examples

    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)

[Package DIAlignR version 2.2.0 Index]