phylogenetics/tools/ancestral_reconstruction.py
def run(df,
        project_dir,
        id_col='uid',
        sequence_col='sequence',
        altall_cutoff=0.2,
        aaRatefile='lg',
        **kwargs):
    """
    Run ancestral sequence reconstruction powered by PAML.
    """

    reconstruction_df = pyasr.reconstruct(
        df,
        id_col=id_col,
        working_dir=project_dir,
        sequence_col=sequence_col,
        altall_cutoff=altall_cutoff,
        aaRatefile=aaRatefile,
        **kwargs
    )

    return reconstruction_df

    Run ancestral sequence reconstruction powered by PAML.
    
Run ancestral sequence reconstruction powered by PAML.
Run ancestral sequence reconstruction powered by PAML .
def run(df,
        project_dir,
        id_col='uid',
        sequence_col='sequence',
        altall_cutoff=0.2,
        aaRatefile='lg',
        **kwargs):
    reconstruction_df = pyasr.reconstruct(
        df,
        id_col=id_col,
        working_dir=project_dir,
        sequence_col=sequence_col,
        altall_cutoff=altall_cutoff,
        aaRatefile=aaRatefile,
        **kwargs
    )
    return reconstruction_df
def run ( df , project_dir , id_col = 'uid' , sequence_col = 'sequence' , altall_cutoff = 0.2 , aaRatefile = 'lg' , ** kwargs ) : reconstruction_df = pyasr . reconstruct ( df , id_col = id_col , working_dir = project_dir , sequence_col = sequence_col , altall_cutoff = altall_cutoff , aaRatefile = aaRatefile , ** kwargs ) return reconstruction_df
Run ancestral sequence reconstruction powered by PAML.
Run ancestral sequence reconstruction powered by PAML .
"""
    Run ancestral sequence reconstruction powered by PAML.
    """
df
project_dir
id_col
sequence_col
altall_cutoff
aaRatefile