## Orthologs.Align.ClustalO


Align genes using Clustal Omega.


Usage

``` python
Orthologs.Align.ClustalO(
    infile,
    outfile,
    logpath=None,
    outfmt="fasta",
)
```


This class is a further wrapper around Biopython's ClustalOmegaCommandline.


## Parameters


`infile: str`  
Path/Name of multiple fasta file.

`outfile: str`  
Path/Name of multiple alignment file.

`logpath: str | None = None`  
Path to logfile.

`outfmt: str = ``"fasta"`  
Format of the output multiple alignment file (e.g., 'fasta', 'clustal', 'phylip').


## Methods

| Name | Description |
|----|----|
| [__init__()](#__init__) | Set up the logger and the parameters. |
| [runclustalomega()](#runclustalomega) | Run Clustal Omega alignment. |

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


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


Set up the logger and the parameters.


Usage

``` python
__init__(infile, outfile, logpath=None, outfmt="fasta")
```


##### Parameters


`infile: str`  
Path/Name of multiple fasta file.

`outfile: str`  
Path/Name of multiple alignment file.

`logpath: str | None = None`  
Path to logfile.

`outfmt: str = ``"fasta"`  
Format of the output multiple alignment file.


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


#### runclustalomega()


Run Clustal Omega alignment.


Usage

``` python
runclustalomega()
```


Executes the Clustal Omega command line tool to perform multiple sequence alignment on the input file.