Hi All,
I'm just submitting this request again, in case someone has a solution,
but I caught them at a bad time.
Any help would be greatly appreciated.
Cheers,
Alastair
On 2011/05/08 04:10 PM, Alastair Potts wrote:
Good day all,
I have been trying to figure out how the nodes and edges are
Hi,
I wrote a code some times ago to do this. It perhaps needs to be adapted.
Do not hesitate to ask if it is not clear.
library(ape)
#===FONCTION=
`edgeAttributes` -
function(node.values, tree,
All,
I have a tree topology (tree_name.tre), and a distance matrix, based
on that tree topology. However I cant not seem to find the nexus file
from which the matrix was generated. Is there a way to use that
distance matrix to incorporate branch lengths into my topology?
I have looked into all
Hi Nick,
I tried nj, but the topology I obtain from that is totally different.
I am not sure if it has anything to do with the fact that the tree was
created based on maximum likelihood?
Thanks though!
Meche
On Thu, May 12, 2011 at 4:23 PM, Nick Matzke mat...@berkeley.edu wrote:
The APE
You can get the least squares branch lengths. I believe that if the
distance matrix is a patristic distance matrix from your tree, then the
least squares branch lengths are guaranteed to be the same as your
original branches (and you should have a sum of squares error, Q, of
zero - to
The APE command NJ (neighbor-joining) will form a tree from
a distance matrix, so that's one option. You could do it
and then see if you get the same topology from NJ as from
your topology tree. The branch lengths will reflect
whatever distances were calculated from the data (which
might be
