Clustal Omega is a fast and scalable tool that makes multiple sequence alignments of protein sequences. For more information, see the tool's homepage.

Function Call

tc.clustalo(
    inputs,
    output_path=None,
    tool_args="",
    is_async=False,
)

Function Arguments

See the Notes section below for more details.

Argument	Use in place of:	Description
inputs	-i	Path to one or more files to use as input. The files can be a local or remote, see Using Files.
output_path	-o	(optional) Path (directory) to where the output files will be downloaded. If omitted, skips download. The files can be a local or remote, see Using Files.
tool_args	all other arguments	(optional) Additional arguments to be passed to Clustal Omega. This should be a string of arguments like the command line. See Supported Additional Arguments for more details.
is_async		Whether to run a job asynchronously. See Async Runs for more.

Tool Versions

Toolchest currently supports version 1.2.4 of Clustal Omega.

Supported Additional Arguments

• --auto
• --dealign
• --infmt
• --is-profile
• --iter
• --iterations
• --max-guidetree-iterations
• --max-hmm-iterations
• --maxnumseq
• --maxseqlen
• --outfmt
• --output-order
• --residuenumber
• --resno
• --seqtype
• -t
• --wrap

Additional arguments can be specified under the tool_args argument.