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What can I do with ClustalW?

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What can I do with ClustalW?

The program ClustalW can be used for two purposes:

1. It can be used to produce a multiple sequence alignment. Using the web form the user need only input or upload a file of the sequences that they want to align in an accepted format. The other options on the form are set to the default values for producing a multiple alignment. The user can use the defaults or they can make some changes on the form to customise their run. A multiple sequence alignment of the sequences submitted will be returned to the user (.aln file).

2. It can be used to produce a true phylogenetic tree. In order to use this option, the user must input or upload a multiple alignment of sequences in one of the standard multiple alignment formats (.aln file). Then, in the phylogentic tree section of the form, they must choose one of the tree type options; NJ, Pyhlip or Dist. These are programs for drawing phylogenetic trees. This time the user will retrieve a .ph (always), .dst and/or .nj files (depending on options chosen), which will contain the phylogenetic trees.

By default, the form is set to produce a multiple alignment.

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