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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


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.