Question: R: Ape Making An Ultrametric, Rooted, Binary Tree Which Can Be Converted Into An R Dendrogram Object
2
gravatar for Timtico
8.7 years ago by
Timtico330
NL
Timtico330 wrote:

Dear all,

I realize that this question might be very (too) specific but I hope someone can help me out here. I'm trying to build a phylogenetic treeusing ClustalW2 (protein), and convert this into an R dendrogram object. This dendrogram object I want to use to rearrange some heatmaps I have (expression / labdata).

I use the ape package to read in the treefile that clustal (EBI) outputs in Phylip format. after this i define the outgroup and try to get it ultrametric using a Sanderson molecular aging algorithm (chronopl in the ape package). I need the tree to be ultrametric, rooted and binary to be able to convert it into an R dendrogram using the as.hclust.phylo function. Here is some R code (I can provide you with the treefile upon request).

require("ape")
library("gplots")


rm(list=ls(all=TRUE))
### read in Phylip guidetree created in ClustalW2
setwd("/Users/Tim/Desktop/DatagatherTransporters/ape/")

sptree <- read.tree(file = "sptree3.phylip", text = NULL, tree.names = NULL, skip = 0,
    comment.char = "#", keep.multi = FALSE)

#plot(sptree, cex = 0.5)
outgroup <- match(c("root1","root2"),sptree$tip.label)
sptree.rooted <- root(sptree,outgroup,node = NULL)

sptree.rooted.ultra <- chronopl(sptree.rooted, 0, age.min = 1, age.max = NULL,node = "root", S = 1, tol = 1e-8,CV = FALSE, eval.max = 500, iter.max = 500)

drop.tip(sptree.rooted.ultra,outgroup)

is.ultrametric(sptree.rooted.ultra)
is.binary.tree(sptree.rooted.ultra)
is.rooted(sptree.rooted.ultra)

> drop.tip(sptree.rooted.ultra,outgroup)
Phylogenetic tree with 126 tips and 125 internal nodes.

Tip labels:
    An01g00340, An07g02420, An02g12160, An07g01230, An11g10600, An17g01560, ...

Rooted; includes branch lengths.
> 
> is.ultrametric(sptree.rooted.ultra)
[1] TRUE
> is.binary.tree(sptree.rooted.ultra)
[1] TRUE
> is.rooted(sptree.rooted.ultra)
[1] FALSE

So, I've been fiddling with the code alot, and at one stage I was able to create a binary, ultrametric, rooted tree. But I'm unable to replicate it using a different treefile. I use an artifical outgroup (root1 and root2) that are two random sequences. They group nicely together.

I hope someone with abit more experience in this. What is the best approach?

All help is much appreciated,

Tim

R phylogenetics • 16k views
ADD COMMENTlink modified 6.7 years ago by Joseph Hughes2.7k • written 8.7 years ago by Timtico330

Why the artificial outgroup? Maybe the error is in how you remove it? Also, what is the result of is.rooted(sptree.rooted) ? Maybe the root function failed for whatever reason - drop.tip should keep the rootedness if the tree is rooted.

ADD REPLYlink written 8.2 years ago by Roman Zenka10
0
gravatar for Joseph Hughes
6.7 years ago by
Joseph Hughes2.7k
Scotland, UK
Joseph Hughes2.7k wrote:

Hi,

I have had similar issues with rooting using root but I got round it using by keeping the basal trichotomy but forcing the tree as rooted:

sptree$root.edge <- 0

I found this in the R help for root. I hope it helps.

ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by Joseph Hughes2.7k
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