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
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