## Orthologs.Phylogenetics.PAML.CodemlRun


Run PAML's codeml program using Biopython's codeml wrapper.


Usage

``` python
Orthologs.Phylogenetics.PAML.CodemlRun(
    P2N_alignment,
    iqtree_newick,
    control_file="codeml-8-11-2017.ctl",
    home=os.getcwd()
)
```


This class sets up the necessary files and configuration for running codeml analysis on a PAL2NAL alignment and IQTree newick tree.


## Methods

| Name | Description |
|----|----|
| [__init__()](#__init__) | Initialize CodemlRun class. |
| [control_setup()](#control_setup) | Set up the codeml control file from template. |

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


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


Initialize CodemlRun class.


Usage

``` python
__init__(
    P2N_alignment,
    iqtree_newick,
    control_file="codeml-8-11-2017.ctl",
    home=os.getcwd()
)
```


##### Parameters


`P2N_alignment: str`  
Path to PAL2NAL alignment file.

`iqtree_newick: str`  
Path to IQTree newick tree file.

`control_file: str = ``"codeml-8-11-2017.ctl"`  
Name of the codeml control file template.

`home: str | Path = os.getcwd()`  
Working directory for codeml execution.


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


#### control_setup()


Set up the codeml control file from template.


Usage

``` python
control_setup(control_template)
```


Reads the control file template, prints options, and writes a gene-specific control file.


##### Parameters


`control_template: str`  
Path to the codeml control file template.