## Orthologs.Align.Pal2NalCommandline


Command line wrapper for PAL2NAL.


Usage

``` python
Orthologs.Align.Pal2NalCommandline(
    cmd="pal2nal",
    **kwargs,
)
```


http://www.bork.embl.de/pal2nal/


## Notes

Last checked against version: v14


Mikita Suyama, David Torrents, and Peer Bork (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Research, 1 July 2006; 34: W609-W612; https://doi.org/10.1093/nar/gkl315


``` python
>>> from Bio.Align.Applications import PAL2NALCommandline
```


## Methods

| Name | Description |
|----|----|
| [__init__()](#__init__) | Initialize PAL2NAL command line wrapper. |

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


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


Initialize PAL2NAL command line wrapper.


Usage

``` python
__init__(cmd="pal2nal", **kwargs)
```


##### Parameters


`cmd: str = ``"pal2nal"`  
Command name for PAL2NAL executable.

`kwargs: dict = {}`  
Parameters for PAL2NAL configuration including:

- pepaln: Protein alignment file (required)
- nucfasta: DNA sequences file (required)
- output: Output format (clustal\|paml\|fasta\|codon)
- output_file: Output file path (required)
- nogap: Remove gaps and stop codons (switch)
- nomismatch: Remove mismatched codons (switch)
- codontable: Genetic code table number (optional)