Create A Consensus Tree From Multiphylo Objects- Ape Package

Question

[Agatha]

Hello,

I would like to generate a skyline plot with coalescent intervals (using "ape" package). I am reading the file using read.nexus function and I have stored them in a list.

summary(my_list)
Length Class      Mode
[1,] 10     multiPhylo list

I tried to use the consensus function to create a consensus tree. However, when I try to plot it- using the regular plot function, the tree is unrooted and all the branches have the same length.

Is there a way to create the consensus tree for my NEXUS files correctly?

Cheers!

Answer 1

[David W]

Most methods to make consensus trees will only give you the topology (all branch lengths equal), partly becuase it's hard to know how you should assign branch lengths to the consensus when some of the trees won't have had the particular pairing.

If you like the consensus tree,and want to add branch lengths to it, you can use it as a starting tree and estimate only the branch lengths from your data (this is documented in most phylogeny packages). But if you are aiming for a skyline plot that incorporates the uncertainty in a phylogenetic estimate, I'd look at the Bayesian skyline in BEAST

[Agatha]

@ david w -Thank you for your reply. Actually the aim for what am I doing was to generate an "average bayesian skyline plot"(similar to the ones that can be created in BEAST) that could summarize the content from a NEXUS file (several trees in my case). This is why I was thinking that maybe I could compute somehow the consensus tree and then plot it using the skyline function - although it is far from being what I would like to have in the end.