phylogeny

Question

[1509636876]

Dear all， I am a student in the field of phylogeny.I calculated the phylogenetic diversity with R Language.I I encountered the above problem.Maybe there's something wrong with my phylogenetic tree.I wish to ask teachers to help me solve this problem.

Thanks a lot！！！

Error in node.age(sub.tree) : 
    function node.age only works with a rooted phylo object

Answer 1

[Dave Carlson]

You should check if your phylogeny is rooted. For example:

install.packages('ape')
library(ape)
mytree <- read.tree(file = "mytree.nwk") # assumes newick format
is.rooted(mytree)

This should return "TRUE" if your phylogeny is indeed rooted.

If it is not rooted, then you will need to root it yourself (e.g., via outgroup, midpoint rooting, etc.). See here for more info:

https://rdrr.io/cran/ape/man/root.html

Answer 2

[1509636876]

Thanks a lot！ Thank you for your help. I have checked my phylogeny and it returned "TRUE",but the problem still occur. I I don't know what went wrong.

library(ape)
mytree<-read.tree(file = "mytree.nwk")
is.rooted(mytree)
[1] TRUE
library(picante)
sam<-readsample("sample.txt")
ses.pd(sam,mytree,null.model = "phylogeny.pool",runs=99)

Error in node.age(sub.tree) : function node.age only works with a rooted phylo object

[炫]

您好，我的问题和您的一模一样，请问您这个问题最终解决了吗

[炫]

Hello, my problem is the same as yours, did you finally solve this problem?

Answer 3

[1509636876]

May be because it can't be calculated all at once, but in batches

[sk_cheung]

What did you mean? btw I got the same problem, and I don't know how to solve?