omicverse.alignment.fasttree

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omicverse.alignment.fasttree#

omicverse.alignment.fasttree(aligned_fasta, output_dir, output_name='tree.nwk', model='gtr', gamma=True, nt=True, threads=None, extra_args=None, fasttree_path=None, auto_install=True, overwrite=False)[source]#

Run FastTree to infer a phylogenetic tree.

Parameters:

  • aligned_fasta (str)

  • output_dir (str)

  • output_name (str (default: 'tree.nwk'))

  • model (str (default: 'gtr'))

  • gamma (bool (default: True))

  • nt (bool (default: True))

  • threads (Optional[int] (default: None))

  • extra_args (Optional[Sequence[str]] (default: None))

  • fasttree_path (Optional[str] (default: None))

  • auto_install (bool (default: True))

  • overwrite (bool (default: False))

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