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How display length of branches in phylogenetic tree

Tags:

r

phylogeny

Here I have code that draw simple phylogenetic tree from newick format:

library(ape)
t<-read.tree(text="(F:4,(  (D:2,E:2):1,(C:2,(B:1,A:1):1):1):1);")
plot(t,use.egde.length=TRUE)

i am"displaying" correct length of branches, but i want all branch to have labal with it. enter image description here

edit: i want my plot to look like this: enter image description here I was searching documentation, but I cannot find method to display length of branch in R. How can i do this ?

like image 725
Frederigo Avatar asked Nov 16 '15 08:11

Frederigo


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How do you calculate the length of a branch?

Each height is scaled so that root height is 1, and then raised at power 'rho' (> 0). Branch lengths are then computed as the difference between height of lower node and height of upper node.

What do the length of the branches of the Phylogram represent?

Phylogram: Branch lengths are directly related to the amount of genetic change. The longer the branch of a tree, the greater the amount of phylogenetic change that has taken place.

What does a Long branch on a phylogenetic tree mean?

Phylogenetic Systematics Sometimes, e.g., with molecular sequence data, one or more taxa will have a very long branch, meaning that these taxa have a large number of autapomorphies relative to other taxa in the analysis (e.g., taxon Z of Figure 2.14D).

Does length matter in phylogenetic tree?

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1 Answers

You can do it by extracting edge lengths and using edgelabels().

# Load package
library(ape)

# Create data
t <- read.tree(text="(F:4,((D:2,E:2):1,(C:2,(B:1,A:1):1):1):1);")
plot(t)
edgelabels(t$edge.length, bg="black", col="white", font=2)

like image 167
Slow loris Avatar answered Sep 25 '22 00:09

Slow loris