phylogenetic_treeを書き換えました

Sure, when you are submitting a pull request for your phylogenetic_tree.py script, you can describe the changes you made based on our discussion as follows:

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Description of Changes

1. Importing MultipleSeqAlignment from Bio.Align To resolve the TypeError encountered initially, we imported the MultipleSeqAlignment class from Bio.Align. This allowed us to create a MultipleSeqAlignment object using the sequence data read from the FASTA file, which is the correct type of object to pass to the get_distance method.

   from Bio.Align import MultipleSeqAlignment

2. Creating a MultipleSeqAlignment Object We updated the alignment variable to be a MultipleSeqAlignment object created from the list of SeqRecord objects returned by SeqIO.parse. This ensures compatibility with the get_distance method from Bio.Phylo.TreeConstruction.

   alignment = MultipleSeqAlignment(list(SeqIO.parse(fasta_file, "fasta")))

3. Saving the Phylogenetic Tree as a PNG File To enable the saving of the phylogenetic tree as a PNG file, we introduced matplotlib to draw and save the tree diagram. We created a new figure and axes using plt.subplots() before calling Phylo.draw, and specified the axes where the tree should be drawn using the axes parameter of Phylo.draw. Finally, we used plt.savefig to save the phylogenetic tree as a PNG file in the current working directory.

   import matplotlib.pyplot as plt
   
   # ... (other parts of the script)
   
   fig, ax = plt.subplots()
   Phylo.draw(tree, axes=ax)
   plt.savefig('phylogenetic_tree.png')

Additional Note

Ensure to install the matplotlib library in your Python environment to avoid a MissingPythonDependencyError. You can install it using the following command:

pip install matplotlib

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Make sure to include the updated script file in your pull request. This description outlines the changes made to the script and provides the rationale behind each change, making it clear to reviewers why each change was necessary.