|creating tree from distance matrix||kaustubh.patil||3/5/12 3:09 PM|
First of all I would like to thank for the nice software.
I want to compare trees created by two distance matrices. DendroPy
provides a way to compare trees but I could not find a way create a
tree from distance matrix (e.g. NJ). Is there a way to do this, my
apologies if I missed it.
PS: currently I am creating tree in PyCogent and then reading is as
Newick in DendroPy to compare them, which slows down things as I want
to do this for thousands of trees.
|Re: creating tree from distance matrix||Jeet Sukumaran||3/7/12 10:23 AM|
The dendropy.interop.paup.estimate_tree() function will allow you to
do this if you have PAUP* available on your system:
from dendropy.interpop import paup
(read data into `char_matrix`)
tree = paup.estimate_tree(char_matrix, 'nj')
|Re: creating tree from distance matrix||ifreak||11/14/12 3:05 AM|
Hi, i was trying your suggestion.
first of all there is an error : from dendropy.interpop import paup should be -> from dendropy.interop import paup
and secondly, i have distance matrix as follows inside a numpy array:
[[ 0 2 7 8 16 17]
[ 2 0 5 6 17 16]
[ 7 5 0 9 15 13]
[ 8 6 9 0 18 16]
[16 17 15 18 0 5]
[17 16 13 16 5 0]]
how can i generate the tree from it using your method. thank you
|Re: creating tree from distance matrix||Giulio Valentino Dalla Riva||6/27/13 9:31 PM|
Did you figured out how to do it?