## Orthologs.Phylogenetics.FilteredTree


Run IQTree to generate a "filtered" tree or best tree.


Usage

``` python
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__()](#__init__) | Initialize FilteredTree class. |
| [iqtree_best_tree()](#iqtree_best_tree) | Generate and save the best tree from IQTree by importing the filtered alignment. |

------------------------------------------------------------------------


#### \_\_init\_\_()


Initialize FilteredTree class.


Usage

``` python
__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

``` python
iqtree_best_tree(alignment, dataType)
```


##### Parameters


`alignment: str`  
Path to multiple sequence alignment file.

`dataType: str`  
Input datatype for IQTree.