Dear Scott,
What should branch lengths on a consensus tree represent?
They cannot be expected substitutions per residue. This would imply no
evolution at points where uncertain branching patterns have been reduced
to a multi-furcation - which is not what the multi-furcation is meant to
imply. (Rather: there was evolution, but we aren't very certain about the
branching pattern.)
But, MrBayes does provide average lengths of some kind.
Best wishes,
Daniel
On 21/11/2012 15:13, "Scott Chamberlain" <myrmecocys...@gmail.com> wrote:
>When making a consensus tree using ape::consensus the branch lengths are
>lost. Is there a way to not lose the branch lengths? Or to add them
>somehow
>to the consensus tree after making it.
>
>library(ape)
>>
>>cat("owls(((Strix_aluco:4.2,Asio_otus:4.1):4.1,Athene_noctua:7.3):6.3,Tyt
>>o_alba:13.5);", file = "ex1.tre", sep = "\n")>
>>cat("owls(((Strix_aluco:1.2,Asio_otus:4.5):3.1,Athene_noctua:7.3):6.3,Tyt
>>o_alba:13.5);", file = "ex2.tre", sep = "\n")>
>>cat("owls(((Strix_aluco:3.2,Asio_otus:4.7):8.1,Athene_noctua:7.3):6.3,Tyt
>>o_alba:13.5);", file = "ex3.tre", sep = "\n")> tree1 <-
>>read.tree("ex1.tre")> tree2 <- read.tree("ex2.tre")> tree3 <-
>>read.tree("ex3.tre")> trees <- c(tree1, tree2, tree3)> trees_con <-
>>consensus(trees)> trees_con
>Phylogenetic tree with 4 tips and 3 internal nodes.
>Tip labels:[1] "Strix_aluco" "Asio_otus" "Athene_noctua" "Tyto_alba"
>Rooted; no branch lengths.
>
>
>Thanks, Scott Chamberlain
>
> [[alternative HTML version deleted]]
>
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--
Daniel Barker
http://bio.st-andrews.ac.uk/staff/db60.htm
The University of St Andrews is a charity registered in Scotland : No
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