Orthologs.Align.ClustalO

Align genes using Clustal Omega.

Usage

Source

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__()	Set up the logger and the parameters.
runclustalomega()	Run Clustal Omega alignment.

---

__init__()

Set up the logger and the parameters.

Usage

Source

__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

Source

runclustalomega()

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