In [1]:

    

from __future__ import print_function
import os
import shutil

import dendropy
from dendropy.interop import raxml


    

In [2]:

    

ebola_data = dendropy.DnaCharacterMatrix.get_from_path('trim.fasta', 'fasta')
rx = raxml.RaxmlRunner()
ebola_tree = rx.estimate_tree(ebola_data, ['-m', 'GTRGAMMA', '-N', '10'])
print('RAxML temporary directory: %s' % rx.working_dir_path)
del ebola_data


    

    




/tmp/tmp3_S6zS

In [3]:

    

ebola_tree.write_to_path('my_ebola.nex', 'nexus')


    

In [4]:

    

import matplotlib.pyplot as plt
from Bio import Phylo
%matplotlib inline
my_ebola_tree = Phylo.read('my_ebola.nex', 'nexus')
my_ebola_tree.name = 'Our Ebolavirus tree'

fig = plt.figure(figsize=(16, 18))
ax = fig.add_subplot(1, 1, 1)
Phylo.draw(my_ebola_tree, axes=ax)


    

In [5]:

    

import random
import sys
from Bio.Phylo.Applications import RaxmlCommandline
raxml_cline = RaxmlCommandline(sequences='trim.fasta',
                               model='GTRGAMMA', name='biopython',
                               num_replicates='10',
                               parsimony_seed=random.randint(0, sys.maxint),
                               working_dir=os.getcwd() + os.sep + 'bp_rx')
print(raxml_cline)
try:
    os.mkdir('bp_rx')
except OSError:
    shutil.rmtree('bp_rx')
    os.mkdir('bp_rx')
out, err = raxml_cline()


    

    




raxmlHPC -m GTRGAMMA -n biopython -p 7472159317643208929 -s trim.fasta -w /home/tra/bioinf-python/notebooks/05_Phylo/bp_rx -N 10

In [6]:

    

from Bio import Phylo
biopython_tree = Phylo.read('bp_rx/RAxML_bestTree.biopython', 'newick')


    

In [7]:

    

print(biopython_tree)


    

    




Tree(rooted=False, weight=1.0)
    Clade(branch_length=0.0)
        Clade(branch_length=0.000194160545644)
            Clade(branch_length=0.00750724471696)
                Clade(branch_length=0.00849916806279, name='BDBV_FJ217161')
                Clade(branch_length=0.461045620814)
                    Clade(branch_length=0.488266643512, name='TAFV_FJ217162')
                    Clade(branch_length=0.428082521767)
                        Clade(branch_length=0.387350036187)
                            Clade(branch_length=1.04377599779)
                                Clade(branch_length=0.0335449613519)
                                    Clade(branch_length=0.00192035471481)
                                        Clade(branch_length=0.00426943306622, name='SUDV_JN638998')
                                        Clade(branch_length=0.00304784447369, name='SUDV_AY729654')
                                    Clade(branch_length=0.00498128112027, name='SUDV_KC589025')
                                Clade(branch_length=0.0257813689425)
                                    Clade(branch_length=0.00286330169986, name='SUDV_EU338380')
                                    Clade(branch_length=0.000182854753968)
                                        Clade(branch_length=0.00106022542422, name='SUDV_FJ968794')
                                        Clade(branch_length=0.0014474653132, name='SUDV_KC242783')
                            Clade(branch_length=0.911922905889)
                                Clade(branch_length=0.0204765581693, name='RESTV_FJ621584')
                                Clade(branch_length=0.0163388846864)
                                    Clade(branch_length=0.00493267289878)
                                        Clade(branch_length=0.0133826459032, name='RESTV_FJ621585')
                                        Clade(branch_length=0.00214945974425)
                                            Clade(branch_length=0.000391808706855, name='RESTV_JX477166')
                                            Clade(branch_length=0.000783119104705, name='RESTV_AB050936')
                                    Clade(branch_length=0.0207865248205)
                                        Clade(branch_length=0.000188076767897, name='RESTV_FJ621583')
                                        Clade(branch_length=0.000790513246633, name='RESTV_JX477165')
                        Clade(branch_length=0.519072173248)
                            Clade(branch_length=0.00852806973742)
                                Clade(branch_length=0.00665048264318)
                                    Clade(branch_length=0.00554859879376)
                                        Clade(branch_length=5.70834480136e-05, name='EBOV_1976_KC242801')
                                        Clade(branch_length=0.000650166398369, name='EBOV_1976_AF272001')
                                    Clade(branch_length=0.00858569979187)
                                        Clade(branch_length=6.38986984845e-07, name='EBOV_1995_KC242799')
                                        Clade(branch_length=6.4252600142e-05, name='EBOV_1995_KC242796')
                                Clade(branch_length=0.0109696820943)
                                    Clade(branch_length=6.38986984845e-07)
                                        Clade(branch_length=0.000257115508926, name='EBOV_2007_KC242784')
                                        Clade(branch_length=6.38986984845e-07)
                                            Clade(branch_length=6.42631955345e-05)
                                                Clade(branch_length=6.38986984845e-07, name='EBOV_2007_KC242787')
                                                Clade(branch_length=0.000514384020052, name='EBOV_2007_KC242788')
                                            Clade(branch_length=6.42665892197e-05)
                                                Clade(branch_length=0.000192820455659, name='EBOV_2007_KC242785')
                                                Clade(branch_length=0.000257120008617, name='EBOV_2007_KC242790')
                                    Clade(branch_length=6.42635971398e-05)
                                        Clade(branch_length=6.42697168931e-05, name='EBOV_2007_KC242786')
                                        Clade(branch_length=0.000128537990573, name='EBOV_2007_KC242789')
                            Clade(branch_length=0.0158963970546)
                                Clade(branch_length=6.38986984845e-07)
                                    Clade(branch_length=6.38986984845e-07)
                                        Clade(branch_length=6.38986984845e-07)
                                            Clade(branch_length=6.38986984845e-07, name='EBOV_2014_KM034554')
                                            Clade(branch_length=6.38986984845e-07)
                                                Clade(branch_length=6.42718890129e-05, name='EBOV_2014_KM034561')
                                                Clade(branch_length=6.38986984845e-07)
                                                    Clade(branch_length=6.38986984845e-07)
                                                        Clade(branch_length=6.38986984845e-07, name='EBOV_2014_KM034549')
                                                        Clade(branch_length=6.62327959856e-05, name='EBOV_2014_KM034563')
                                                    Clade(branch_length=6.38986984845e-07, name='EBOV_2014_KM034550')
                                        Clade(branch_length=6.38986984845e-07, name='EBOV_2014_KM034555')
                                    Clade(branch_length=6.38986984845e-07)
                                        Clade(branch_length=0.000257073549015)
                                            Clade(branch_length=6.38986984845e-07)
                                                Clade(branch_length=6.38986984845e-07)
                                                    Clade(branch_length=6.38986984845e-07, name='EBOV_2014_KM034556')
                                                    Clade(branch_length=6.38986984845e-07)
                                                        Clade(branch_length=6.38986984845e-07, name='EBOV_2014_KM034560')
                                                        Clade(branch_length=6.38986984845e-07)
                                                            Clade(branch_length=0.000128511751436)
                                                                Clade(branch_length=6.38986984845e-07, name='EBOV_2014_KM034558')
                                                                Clade(branch_length=6.38986984845e-07, name='EBOV_2014_KM034551')
                                                            Clade(branch_length=6.38986984845e-07, name='EBOV_2014_KM034552')
                                                Clade(branch_length=6.38986984845e-07, name='EBOV_2014_KM034557')
                                            Clade(branch_length=0.0001285138714, name='EBOV_2014_KM034553')
                                        Clade(branch_length=0.000128516186276, name='EBOV_2014_KM034562')
                                Clade(branch_length=6.42081344029e-05, name='EBOV_2014_KM034559')
            Clade(branch_length=0.000131394352753, name='BDBV_KC545396')
        Clade(branch_length=6.38986984845e-07)
            Clade(branch_length=0.000130195141019, name='BDBV_KC545395')
            Clade(branch_length=0.000195337907246, name='BDBV_KC545394')
        Clade(branch_length=0.000130193592898, name='BDBV_KC545393')

In [ ]: