## Orthologs.Align.Guidance2Commandline


Command line wrapper for GUIDANCE2.


Usage

``` python
Orthologs.Align.Guidance2Commandline(
    cmd="guidance",
    align=True,
    **kwargs,
)
```


http://guidance.tau.ac.il/ver2/


\>\>\> from Bio.Align.Applications import Guidance2Commandline

You would typically run the command line with clustalomega_cline() or via the Python subprocess module, as described in the Biopython tutorial.


    Sela, I., Ashkenazy, H., Katoh, K. and Pupko, T. (2015)
    GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters.
    Nucleic Acids Research, 2015 Jul 1; 43 (Web Server issue): W7-W14.; doi: 10.1093/nar/gkq443

    Landan, G., and D. Graur. (2008).
    Local reliability measures from sets of co-optimal multiple sequence alignments.
    Pac Symp Biocomput 13:15-24


## Methods

| Name | Description |
|----|----|
| [__init__()](#__init__) | Initialize GUIDANCE2 command line wrapper. |

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


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


Initialize GUIDANCE2 command line wrapper.


Usage

``` python
__init__(cmd="guidance", align=True, **kwargs)
```


##### Parameters


`cmd: str = ``"guidance"`  
Command name for GUIDANCE2 executable.

`align: bool = ``True`  
Flag to determine if alignment mode is used.

`kwargs: object = {}`  
Additional parameters for GUIDANCE2 configuration.