Hello,
I've been trying to figure out how to access the individual elements
from an object of class phylo.
I am reading in 201 trees created by paup as below.
> read.nexus("A_30knj_200t.txt", tree.names= NULL) -> anj30
> anj30[1]
$tree1
$edge
[,1] [,2]
[1,] "-1" "-2"
[2,] "-2" "-3"
[3,] "-3" "1"
[4,] "-3" "2"
[5,] "-2" "-4"
[6,] "-4" "3"
[7,] "-4" "4"
[8,] "-1" "-5"
[9,] "-5" "-6"
[10,] "-6" "5"
[11,] "-6" "6"
[12,] "-5" "7"
$edge.length
[1] 0.00000 0.00412 0.01012 0.00625 0.00576 0.00519 0.00536 0.01817
0.00713 0.00772 0.00913 0.01506
$tip.label
[1] "H" "G" "F" "E" "D" "C" "B"
attr(,"class")
[1] "phylo"
The only problem is i can't access or save the individual trees after
importing. What i want to do is calculate the cophenetic distance for
each tree and take the correlation between pairs of trees. I keep
getting errors like this:
x<- anj30[1]
> class(x)
[1] "list"
> as.phylo(x)
Error in as.phylo(x) : no applicable method for "as.phylo"
> cophenetic.phylo(x)
Error in cophenetic.phylo(x) : your tree has no branch lengths defined
and
> cophenetic.phylo(anj30[1])
Error in cophenetic.phylo(anj30[1]) : your tree has no branch lengths defined
If i paste the tree directly into read.tree() on the console then it
works but I can't do this for thousands of trees ( which i have to
process according to my PhD committee :) )
Does anyone know how to get the individual trees into usable variables?
I apologize for my lack of familiarity with the package.
thanks,
betty
--
Betty Gilbert
[EMAIL PROTECTED]
Taylor Lab
Plant and Microbial Biology
321 Koshland Hall
U.C. Berkeley
Berkeley, Ca 94720
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