clustalo -h

Clustal Omega - 1.2.4 (AndreaGiacomo)

If you like Clustal-Omega please cite:

Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG.

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.

Mol Syst Biol. 2011 Oct 11;7:539. doi: 10.1038/msb.2011.75. PMID: 21988835.

If you don't like Clustal-Omega, please let us know why (and cite us anyway).

Check http://www.clustal.org for more information and updates.

Usage: clustalo [-hv] [-i {<file>,-}] [--hmm-in=<file>]... [--hmm-batch=<file>] [--dealign] [--profile1=<file>] [--profile2=<file>] [--is-profile][-t {Protein, RNA, DNA}] [--infmt={a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]}] [--distmat-in=<file>] [--distmat-out=<file>] [--guidetree-in=<file>] [--guidetree-out=<file>] [--pileup] [--full] [--full-iter] [--cluster-size=<n>] [--clustering-out=<file>] [--trans=<n>] [--posterior-out=<file>] [--use-kimura] [--percent-id] [-o {file,-}] [--outfmt={a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]}] [--residuenumber] [--wrap=<n>] [--output-order={input-order,tree-order}] [--iterations=<n>] [--max-guidetree-iterations=<n>] [--max-hmm-iterations=<n>] [--maxnumseq=<n>] [--maxseqlen=<l>] [--auto] [--threads=<n>] [--pseudo=<file>] [-l <file>] [--version] [--long-version] [--force] [--MAC-RAM=<n>]

A typical invocation would be: clustalo -i my-in-seqs.fa -o my-out-seqs.fa -v

See below for a list of all options.

Sequence Input:

  -i, --in, --infile={<file>,-} Multiple sequence input file (- for stdin)

  --hmm-in=<file>          HMM input files

  --hmm-batch=<file>        specify HMMs for individual sequences

  --dealign                Dealign input sequences

  --profile1, --p1=<file>  Pre-aligned multiple sequence file (aligned columns will be kept fix)

  --profile2, --p2=<file>  Pre-aligned multiple sequence file (aligned columns will be kept fix)

  --is-profile              disable check if profile, force profile (default no)

  -t, --seqtype={Protein, RNA, DNA} Force a sequence type (default: auto)

  --infmt={a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]} Forced sequence input file format (default: auto)

Clustering:

  --distmat-in=<file>      Pairwise distance matrix input file (skips distance computation)

  --distmat-out=<file>      Pairwise distance matrix output file

  --guidetree-in=<file>    Guide tree input file (skips distance computation and guide-tree clustering step)

  --guidetree-out=<file>    Guide tree output file

  --pileup                  Sequentially align sequences

  --full                    Use full distance matrix for guide-tree calculation (might be slow; mBed is default)

  --full-iter              Use full distance matrix for guide-tree calculation during iteration (might be slowish; mBed is default)

  --cluster-size=<n>        soft maximum of sequences in sub-clusters

  --clustering-out=<file>  Clustering output file

  --trans=<n>              use transitivity (default: 0)

  --posterior-out=<file>    Posterior probability output file

  --use-kimura              use Kimura distance correction for aligned sequences (default no)

  --percent-id              convert distances into percent identities (default no)

Alignment Output:

  -o, --out, --outfile={file,-} Multiple sequence alignment output file (default: stdout)

  --outfmt={a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]} MSA output file format (default: fasta)

  --residuenumber, --resno  in Clustal format print residue numbers (default no)

  --wrap=<n>                number of residues before line-wrap in output

  --output-order={input-order,tree-order} MSA output order like in input/guide-tree

Iteration:

  --iterations, --iter=<n>  Number of (combined guide-tree/HMM) iterations

  --max-guidetree-iterations=<n> Maximum number of guidetree iterations

  --max-hmm-iterations=<n>  Maximum number of HMM iterations

Limits (will exit early, if exceeded):

  --maxnumseq=<n>          Maximum allowed number of sequences

  --maxseqlen=<l>          Maximum allowed sequence length

Miscellaneous:

  --auto                    Set options automatically (might overwrite some of your options)

  --threads=<n>            Number of processors to use

  --pseudo=<file>          Input file for pseudo-count parameters

  -l, --log=<file>          Log all non-essential output to this file

  -h, --help                Print this help and exit

  -v, --verbose            Verbose output (increases if given multiple times)

  --version                Print version information and exit

  --long-version            Print long version information and exit

  --force                  Force file overwriting