Orthologs.Phylogenetics.FilteredTree
Run IQTree to generate a “filtered” tree or best tree.
Usage
Orthologs.Phylogenetics.FilteredTree(
alignment, dataType="CODON", home=os.getcwd()
)Parameters
alignment: str-
Path to multiple sequence alignment file.
dataType: str = "CODON"-
Input datatype (e.g., ‘CODON’, ‘DNA’, ‘AA’).
home: str | Path = os.getcwd()- Path of working directory.
Methods
| Name | Description |
|---|---|
| __init__() | Initialize FilteredTree class. |
| iqtree_best_tree() | Generate and save the best tree from IQTree by importing the filtered alignment. |
__init__()
Initialize FilteredTree class.
Usage
__init__(alignment, dataType="CODON", home=os.getcwd())Parameters
alignment: str-
Path to multiple sequence alignment file.
dataType: str = "CODON"-
Input datatype (e.g., ‘CODON’, ‘DNA’, ‘AA’).
home: str | Path = os.getcwd()- Path of working directory.
iqtree_best_tree()
Generate and save the best tree from IQTree by importing the filtered alignment.
Usage
iqtree_best_tree(alignment, dataType)Parameters
alignment: str-
Path to multiple sequence alignment file.
dataType: str- Input datatype for IQTree.