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to DendroPy Users
Hi all,
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.
best regards
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.
Jeet Sukumaran
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Mar 7, 2012, 1:23:32 PM3/7/12
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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')
Abdullah Sahyoun
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Nov 14, 2012, 6:05:47 AM11/14/12
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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: