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phylogeny

Dear all,

I am a student in the field of phylogeny.I calculated the phylogenetic diversity with R Language. 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
phylogenetic-tree diversity
• 4,058 views • link
written by 1509636876 • 1509636876

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

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written by 炫 • 炫

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

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written by 1509636876 • 1509636876

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

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written by sk_cheung • sk_cheung

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

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written by torehoja • torehoja

Maybe it needs to be converted to a binary tree.

library(ape)
mytree<-multi2di.phylo(mytree.tre)
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written by 1509636876 • 1509636876

1 answer

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

• 0 views • link
updated by Ram Ram • written by Dave Carlson Dave Carlson

Thanks a lot!

Thank you for your help. I have checked my phylogeny and it returned TRUE, but the problem still occurs. 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
• 0 views • link
updated by Ram Ram • written by 1509636876 • 1509636876

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