Installed Clustalw

We have currently installed the version 1.83 of ClustalW.
The reference for this tool is:
Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice.  Nucleic Acids Research, 22:4673-4680.

The officical ClustalW Help page is available on this link.

Help for the Bioinformatica ClustalW

1. Sequence type: select the type of your sequence, protein or dna.
2. Select the algorithm: FAST or SLOW. The correct options will be highlighted.
1. FAST Algorithm:  fast pairwise alignment options
   
   • KTUP: choose which 'word-length' to use when calculating fast pairwise alignments
   • Windows length: Set the window length
     
   • Score: select which score to take into account.
     
   • TopDiag: select here how many top diagonals should be integrated
   • PairGap: set the gap penalty
     
   • Matrix
   • GapOpen
   • GapExt
     
2. SLOW Algorithm: slow and more accurate pairwise alignments options
   • Matrix:  choose which matrix series to use.
     
   • GapOpen: set the penalty for opening a gap.
     
   • EndGap: set the penalty for closing a gap.
     
   • GapExt: penalty for extending a gap.
     
   • GapDist: gap separation penalty
     
3. Alignment or Phylogenetic tree:
1. Alignment: ClustalW can produce different type of output, and order of the sequence in the ouptut: field between:
   • In the Format list the user can choose between: aln with numbers (default), aln without numbers, gcg MSF, phylip, pir and gde.
   • In the Order list, the user can choose beween: the order that the sequences appear in the alignment: aligned (default) or in the order in which they were input.
   • At the same time of the alignment, ClustalW produce a guide tree. This tree can be seen either as a text file or an image, in the PNG format.
     
2. Phylogenetic tree: A guide tree is calculated based on the distance matrix that is generated from the pairwise scores. The output can be found in the .dnd file. A phylogenetic tree is calculated based on the multiple alignment that it receives. The distances between the sequences in the alignment are calculated and can be found in the .ph file. These distances are then used by the method chosen (nj, phylip, dist) to make the phylogenetic tree (.nj, .ph, .dst file).  When you check the box for the phylogenetic tree, the  following options become available:
   
   • Tree : select the method to make the tree
   • Kimura: This options allows you to set on distances correction (correction for multiple substitutions). This is because, as sequences diverge, more than one substitution will happen at many sites. However, you only see one difference when you look at the present day sequences. Therefore, this option has the effect of stretching branch lengths in trees (especially long branches). The corrections used here (for DNA or proteins) are both due to Motoo Kimura.

   • Ignore gaps: Ignore gaps in alignment. The areas of th ealignemt which have many gaps (thus ambiguous) will be ignored. Be careful that if there are many gaps in your alignments, you will throw away a lot of data.
     
   • Image fromat: the current format for the tree image is PNG.
     
4. Paste a sequence or load a file: ClustalW will accept files in the FASTA format. The file will first be checked. Files with errors will be rejected. There are currently no limit to the number of sequences or the file size.
   
5. Run Clustal: clustalW will run as a background job. Execution time will depend on your file and the size and number of sequences. You can wait for the results, or if you can save the clustal job ID and retrieve the results at a later time.
6. Results: please follow this link