This is the command clustalw that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
clustalw - Multiple alignment of nucleic acid and protein sequences
SYNOPSIS
clustalw [-infile] file.ext [OPTIONS]
clustalw [-help | -fullhelp]
DESCRIPTION
Clustal W is a general purpose multiple alignment program for DNA or proteins.
The program performs simultaneous alignment of many nucleotide or amino acid sequences. It
is typically run interactively, providing a menu and an online help. If you prefer to use
it in command-line (batch) mode, you will have to give several options, the minimum being
-infile.
OPTIONS
DATA (sequences)
-infile=file.ext
Input sequences.
-profile1=file.ext and -profile2=file.ext
Profiles (old alignment)
VERBS (do things)
-options
List the command line parameters.
-help or -check
Outline the command line params.
-fullhelp
Output full help content.
-align
Do full multiple alignment.
-tree
Calculate NJ tree.
-pim
Output percent identity matrix (while calculating the tree).
-bootstrap=n
Bootstrap a NJ tree (n= number of bootstraps; def. = 1000).
-convert
Output the input sequences in a different file format.
PARAMETERS (set things)
General settings:
-interactive
Read command line, then enter normal interactive menus.
-quicktree
Use FAST algorithm for the alignment guide tree.
-type=
PROTEIN or DNA sequences.
-negative
Protein alignment with negative values in matrix.
-outfile=
Sequence alignment file name.
-output=
GCG, GDE, PHYLIP, PIR or NEXUS.
-outputorder=
INPUT or ALIGNED
-case
LOWER or UPPER (for GDE output only).
-seqnos=
OFF or ON (for Clustal output only).
-seqnos_range=
OFF or ON (NEW: for all output formats).
-range=m,n
Sequence range to write starting m to m+n.
-maxseqlen=n
Maximum allowed input sequence length.
-quiet
Reduce console output to minimum.
-stats=file
Log some alignments statistics to file.
Fast Pairwise Alignments:
-ktuple=n
Word size.
-topdiags=n
Number of best diags.
-window=n
Window around best diags.
-pairgap=n
Gap penalty.
-score
PERCENT or ABSOLUTE.
Slow Pairwise Alignments:
-pwmatrix=
:Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename
-pwdnamatrix=
DNA weight matrix=BLOSUMIUB, BLOSUMCLUSTALW or BLOSUMfilename.
-pwgapopen=f
Gap opening penalty.
-pwgapext=f
Gap extension penalty.
Multiple Alignments:
-newtree=
File for new guide tree.
-usetree=
File for old guide tree.
-matrix=
Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename.
-dnamatrix=
DNA weight matrix=IUB, CLUSTALW or filename.
-gapopen=f
Gap opening penalty.
-gapext=f
Gap extension penalty.
-engaps
No end gap separation pen.
-gapdist=n
Gap separation pen. range.
-nogap
Residue-specific gaps off.
-nohgap
Hydrophilic gaps off.
-hgapresidues=
List hydrophilic res.
-maxdiv=n
Percent identity for delay.
-type=
PROTEIN or DNA
-transweight=f
Transitions weighting.
-iteration=
NONE or TREE or ALIGNMENT.
-numiter=n
Maximum number of iterations to perform.
Profile Alignments:
-profile
Merge two alignments by profile alignment.
-newtree1=
File for new guide tree for profile1.
-newtree2=
File for new guide tree for profile2.
-usetree1=
File for old guide tree for profile1.
-usetree2=
File for old guide tree for profile2.
Sequence to Profile Alignments:
-sequences
Sequentially add profile2 sequences to profile1 alignment.
-newtree=
File for new guide tree.
-usetree=
File for old guide tree.
Structure Alignments:
-nosecstr1
Do not use secondary structure-gap penalty mask for profile 1.
-nosecstr2
Do not use secondary structure-gap penalty mask for profile 2.
-secstrout=STRUCTURE or MASK or BOTH or NONE
Output in alignment file.
-helixgap=n
Gap penalty for helix core residues.
-strandgap=n
Gap penalty for strand core residues.
loopgap=n
Gap penalty for loop regions.
-terminalgap=n
Gap penalty for structure termini.
-helixendin=n
Number of residues inside helix to be treated as terminal.
-helixendout=n
Number of residues outside helix to be treated as terminal.
-strandendin=n
Number of residues inside strand to be treated as terminal.
-strandendout=n
Number of residues outside strand to be treated as terminal.
Trees:
-outputtree=nj OR phylip OR dist OR nexus
-seed=n
Seed number for bootstraps.
-kimura
Use Kimura's correction.
-tossgaps
Ignore positions with gaps.
-bootlabels=node
Position of bootstrap values in tree display.
-clustering=
NJ or UPGMA.
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