Ape Leaves An Empty Vector For Bootstrap Values, Why Is This And How Should I Resolve This Issue?

Question

[laemtao]

I have a tree which needs to be rerooted multiple times upon several conditions, one of which is the bootstrap value. Ape leaves an empty vector for the bootstrap value of a root. What is the real bootstrap of this node? Why is this and how should I resolve this issue?

> tree$node
 [1] ""    "96"  "100" "88"  "100" "84"  "48"  "80"  "84"  "76"  "100" "68" 
[13] "36"  "100" "100" "100" "100" "60"  "36"  "88"  "36"  "92"  "48"  "48" 
[25] "100" "40"  "64"  "100" "68"  "88"  "100" "48"  "100" "40" 

> root(tree, node = 42)$node
 [1] "84"  "100" "88"  ""    "96"  "100" "48"  "80"  "84"  "76"  "100" "68" 
[13] "36"  "100" "100" "100" "100" "60"  "36"  "88"  "36"  "92"  "48"  "48" 
[25] "100" "40"  "64"  "100" "68"  "88"  "100" "48"  "100" "40"

[minglei1989]

Hi laemtao,

I met the same problem using ape. Have you resolved this problem? Thank you!

Answer 1

[Josh Herr]

To answer your own question think about how you go about computing a bootstrap value. For example, what do you do to compute bootstrap support? Now think about how would you go about computing a bootstrap value on your root node?

I have a question for you: How does a bootstrap value influence the choice of the root of your phylogeny?

Answer 2

[minglei1989]

Hi all,

I met the same problem as laemtao's. I don't konw how to resolve. Thank you!