class jade.basic.sequence.ClustalRunner.ClustalRunner(fasta_path, clustal_name='clustal_omega', clustal_dir=None)

A very simple class wrapper to run clustal omega.

output_alignment(out_dir, out_name, parellel_process=False)

Configure command line and Run Clustal Omega

set_extra_options(extra_options='')

Set any extra options as a string which will be added to the end of the command line.

set_fasta_path(fasta_path)

Set the fasta path for alignment.

set_hard_wrap(hard_wrap)

Set the number of charactors before clustal will wrap. Usually 60-80.

set_output_format(output_format)

Set the output format

set_threads(threads)

Limit the number of threads for Clustal