Intro to Phylogenetics

In [1]:

    

from phylogenetics import PhylogeneticsProject


    

In [19]:

    

# Initialize
project = PhylogeneticsProject('example', overwrite=True)
# Add an alignment
project.read_data(
    #dtype='tips', 
    path='PF08793_seed.fasta',
    schema='fasta'
)
# Run a tree
project.compute_tree()

# Run a reconstruction
project.compute_reconstruction()


    

In [20]:

    

project.history


    

    
Out[20]:





[{'time': '2018-10-26 17:42:35',
  'method': '<function PhylogeneticsProject.__init__ at 0x7fad1e56a510>',
  'args': "('example',)",
  'kwargs': {'overwrite': True}},
 {'time': '2018-10-26 17:42:36',
  'method': '<function PhylogeneticsProject.read_data at 0x7fad1e56a730>',
  'args': '()',
  'kwargs': {'path': 'PF08793_seed.fasta', 'schema': 'fasta'}},
 {'time': '2018-10-26 17:42:45',
  'method': '<function PhylogeneticsProject.compute_tree at 0x7fad1e56a840>',
  'args': '()',
  'kwargs': {}},
 {'time': '2018-10-26 17:42:45',
  'method': '<function PhylogeneticsProject.compute_reconstruction at 0x7fad1e56a950>',
  'args': '()',
  'kwargs': {}}]

In [14]:

    

project.show()


    

    




------------------------------------------------------------------
AttributeError                   Traceback (most recent call last)
<ipython-input-14-4024daed8255> in <module>
----> 1 project.show()

AttributeError: 'PhylogeneticsProject' object has no attribute 'show'

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