Orthologs.Align.Pal2NalCommandline

Command line wrapper for PAL2NAL.

Usage

Source

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

>>> from Bio.Align.Applications import PAL2NALCommandline

Methods

Name Description
__init__() Initialize PAL2NAL command line wrapper.

__init__()

Initialize PAL2NAL command line wrapper.

Usage

Source

__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)