Clustal W is a general purpose multiple alignment program for DNA or proteins. The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. It is designed to be run interactively, or to assign options via the command line.

Clustalw can be run in two ways on the Helix Systems:

1. Multiple Alignment Workshop. A web interface to Clustalw and other multiple seqence alignment programs.

2. Command-line use on Helix
   For many or large sequences, it is probably better to use the command-line than a web interface. At the helix prompt, type 'clustalw'.

   Version

   Type 'clustalw' on Helix to see the current installed version.

   Sample session (user input in bold):

   helix% clustalw
   
    **************************************************************
    ******** CLUSTAL W (1.83) Multiple Sequence Alignments  ********
    **************************************************************
   
        1. Sequence Input From Disc
        2. Multiple Alignments
        3. Profile / Structure Alignments
        4. Phylogenetic trees
   
        S. Execute a system command
        H. HELP
        X. EXIT (leave program)
   
   Your choice: 1
   
   Sequences should all be in 1 file.
   
   7 formats accepted: 
   NBRF/PIR, EMBL/SwissProt, Pearson (Fasta), GDE, Clustal, GCG/MSF, RSF.
   
   Enter the name of the sequence file: seqs.inp
   
   Sequence format is Pearson
   Sequences assumed to be PROTEIN
   
   Sequence 1: chiins          110 aa
   Sequence 2: xenins          110 aa
   Sequence 3: humins          110 aa
   Sequence 4: monins          110 aa
   Sequence 5: dogins          110 aa
   Sequence 6: hamins          110 aa
   Sequence 7: bovins          110 aa
   Sequence 8: guiins          110 aa
   
    **************************************************************
    ******** CLUSTAL W (1.83) Multiple Sequence Alignments  ********
    **************************************************************
   
        1. Sequence Input From Disc
        2. Multiple Alignments
        3. Profile / Structure Alignments
        4. Phylogenetic trees
   
        S. Execute a system command
        H. HELP
        X. EXIT (leave program)
   
   Your choice: 2
   ****** MULTIPLE ALIGNMENT MENU ******
       1.  Do complete multiple alignment now (Slow/Accurate)
       2.  Produce guide tree file only
       3.  Do alignment using old guide tree file
   
       4.  Toggle Slow/Fast pairwise alignments = SLOW
   
       5.  Pairwise alignment parameters
       6.  Multiple alignment parameters
   
       7.  Reset gaps before alignment? = OFF
       8.  Toggle screen display          = ON
       9.  Output format options
   
       S.  Execute a system command
       H.  HELP
       or press [RETURN] to go back to main menu
   
   Your choice: 1
   
   Enter a name for the CLUSTAL output file  [seqs.aln]: myseqs.aln
   
   Enter name for new GUIDE TREE           file   [seqs.dnd]: 
   
   Start of Pairwise alignments
   Aligning...
   Sequences (1:2) Aligned. Score:  66
   Sequences (1:3) Aligned. Score:  63
   [...]
   Sequences (7:8) Aligned. Score:  61
   Guide tree        file created:   [seqs.dnd]
   Start of Multiple Alignment
   There are 7 groups
   Aligning...
   Group 1: Sequences:   2      Score:2138
   Group 2: Sequences:   2      Score:2373
   Group 3: Sequences:   4      Score:2157
   Group 4: Sequences:   5      Score:2146
   Group 5: Sequences:   6      Score:1971
   Group 6: Sequences:   2      Score:1972
   Group 7: Sequences:   8      Score:1739
   Alignment Score 13222
   
   Consensus length = 110
   CLUSTAL-Alignment file created  [seqs.aln]
   
   CLUSTAL W (1.83) multiple sequence alignment
   
   dogins          MALWMRLLPLLALLALWAPAPTRAFVNQHLCGSHLVEALYLVCGERGFFYTPKARREVED
   bovins          MALWTRLRPLLALLALWPPPPARAFVNQHLCGSHLVEALYLVCGERGFFYTPKARREVEG
   humins          BALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAED
   monins          BALWMRLLPLLALLALWGPDPVPAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAED
   hamins          MTLWMRLLPLLTLLVLWEPNPAQAFVNQHLCGSHLVEALYLVCGERGFFYTPKSRRGVED
   guiins          MALWMHLLTVLALLALWGPNTGQAFVSRHLCGSNLVETLYSVCQDDGFFYIPKDRRELED
   chiins          BALWIRSLPLLALLVFSGPGTSYAAANQHLCGSHLVEALYLVCGERGFFYSPKARRDVEQ
   xenins          BALWMQCLPLVLVLFFSTPNTE-ALVNQHLCGSHLVEALYLVCGDRGFFYYPKVKRDMEQ
                    :** :  .:: :* :  * .  * ..:*****:***:** ** : **** ** :*  * 
   
   dogins          LQVRDVELAGAPGEGGLQPLALEGALQKRGIVEQCCTSICSLYQLENYCN
   bovins          PQVGALELAGGPGAGG-----LEGPPQKRGIVEQCCASVCSLYQLENYCN
   humins          LQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN
   monins          PQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN
   hamins          PQVAQLELGGGPGADDLQTLALEVAQQKRGIVDQCCTSICSLYQLENYCN
   guiins          PQVEQTELGMGLGAGGLQPLALEMALQKRGIVDQCCTGTCTRHQLQSYCN
   chiins          PLVSS---PLRGEAGVLPFQQEEYEKVKRGIVEQCCHNTCSLYQLENYCN
   xenins          ALVSG---PQDNELDGMQLQPQEYQKMKRGIVEQCCHSTCSLFQLESYCN
                     *           .       *    *****:*** . *: .**:.***
   
   Press [RETURN] to continue or  X  to stop: X
   
    **************************************************************
    ******** CLUSTAL W (1.83) Multiple Sequence Alignments  ********
    **************************************************************
   
        1. Sequence Input From Disc
        2. Multiple Alignments
        3. Profile / Structure Alignments
        4. Phylogenetic trees
   
        S. Execute a system command
        H. HELP
        X. EXIT (leave program)
   
   Your choice: x
   

Documentation

• Web-accessible: ClustalW Help
• Thompson, Higgins, and Gibson: CLUSTAL W. Nucleic Acids Res, 22: 4673-80. Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice.