R help - May 2006 - problem accessing trees after read.nexus from ape package

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
lgilbert@berkeley.edu
Taylor Lab
Plant and Microbial Biology
321 Koshland Hall
U.C. Berkeley
Berkeley, Ca 94720
	[[alternative HTML version deleted]]

Betty Gilbert <lgilbert <at> berkeley.edu> writes:
> 
> 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
[snip]
> 
>   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
> 
  (1) using [[ instead of [ will help; [ returns a LIST (possibly just
a one-element list), while [[ returns an ELEMENT of the list.

  e.g.:
> x <- list("a","b","c")
> x[1]
[[1]]
[1] "a"
> class(x[1])
[1] "list"
> x[[1]]
[1] "a"
> class(x[[1]])
[1] "character"


  (2) cophy <- lapply(anj30,cophenetic.phylo) should process all
of your phylogenies and return the answer as a list of cophylogenies.

  good luck,
    Ben Bolker