Multiple Alignment



CLUSTAL 2.1 Multiple Sequence Alignments


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= :CLUSTAL(default), GCG, GDE, PHYLIP, PIR, NEXUS and FASTA
-OUTORDER= :INPUT or ALIGNED
-CASE :LOWER or UPPER (for GDE output only)
-SEQNOS= :OFF or ON (for Clustal output only)
-SEQNO_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= :Log some alignents 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=IUB, CLUSTALW or filename
-PWGAPOPEN=f :gap opening penalty
-PWGAPEXT=f :gap opening 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
-ENDGAPS :no end gap separation pen.
-GAPDIST=n :gap separation pen. range
-NOPGAP :residue-specific gaps off
-NOHGAP :hydrophilic gaps off
-HGAPRESIDUES= :list hydrophilic res.
-MAXDIV=n :% ident. for delay
-TYPE= :PROTEIN or DNA
-TRANSWEIGHT=f :transitions weighting
-ITERATION= :NONE or TREE or ALIGNMENT
-NUMITER=n :maximum number of iterations to perform
-NOWEIGHTS :disable sequence weighting


***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 OR branch :position of bootstrap values in tree display
-CLUSTERING= :NJ or UPGMA

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