In [1]:

    

import dendropy
from dendropy.utility.fileutils import find_files
import numpy as np


    

In [2]:

    

taxa = dendropy.TaxonSet()

pb_o = dendropy.Tree.get_from_path('./Trees/original_tree.tre', 'newick', taxon_set=taxa)


    

In [3]:

    

uolist = find_files(top='Trees/MLE', filename_filter='*b')


    

In [4]:

    

uotrees = [dendropy.Tree.get_from_path(filename,"newick", taxon_set=taxa) for filename in uolist]


    

In [3]:

    

olist = find_files(top='garli_opt/', filename_filter='*.tre')
print olist


    

    




['/home/april/projectfiles/squamates/garli_opt/1.tre', '/home/april/projectfiles/squamates/garli_opt/4.tre', '/home/april/projectfiles/squamates/garli_opt/5.tre', '/home/april/projectfiles/squamates/garli_opt/6.tre', '/home/april/projectfiles/squamates/garli_opt/MLE.tre']

In [ ]:

    

otrees = [dendropy.Tree.get_from_path(filename, "nexus") for filename in olist]


    

In [ ]:

    

n = len(uotrees)
udiffarray = np.zeros((n,n))

for i, ele1 in enumerate(uotrees):
    for j, ele2 in enumerate(uotrees):
        if j >= i:
            break # Since the matrix is symmetrical we don't need to
                  # calculate everything
        difference = ele1.symmetric_difference(ele2) 
        udiffarray[i, j] = difference
        udiffarray[j, i] = difference


    

In [ ]:

    

diffarray


    

In [38]:

    

diffarray


    

    
Out[38]:





array([[    0.,   866.,   974.,   886.,  1002.,   884.,   984.,   938.,
          946.],
       [  866.,     0.,   716.,   686.,   632.,   604.,   658.,   700.,
          654.],
       [  974.,   716.,     0.,   718.,   682.,   696.,   794.,   756.,
          784.],
       [  886.,   686.,   718.,     0.,   800.,   692.,   696.,   758.,
          762.],
       [ 1002.,   632.,   682.,   800.,     0.,   618.,   808.,   810.,
          674.],
       [  884.,   604.,   696.,   692.,   618.,     0.,   754.,   696.,
          686.],
       [  984.,   658.,   794.,   696.,   808.,   754.,     0.,   720.,
          714.],
       [  938.,   700.,   756.,   758.,   810.,   696.,   720.,     0.,
          772.],
       [  946.,   654.,   784.,   762.,   674.,   686.,   714.,   772.,
            0.]])

In [36]:

    

o_tl = [tree.length() for tree in otrees]
print o_tl


    

    




[267.81482687115044, 204.3680261301375, 218.91695960755754, 205.61858615952585, 215.44145413795812, 203.79452107889662, 203.37676965100104, 205.6211342413188, 203.61742308190165]

In [39]:

    

uo_tl = [mle.length() for mle in uotrees]
print uo_tl


    

    




[267.81482687115044, 204.3680261301375, 218.91695960755754, 205.61858615952585, 215.44145413795812, 203.79452107889662, 203.37676965100104, 205.6211342413188, 203.61742308190165]

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