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ClustalW FAQ (Frequently Asked Questions)
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- Why use ClustalW?
- How can I use ClustalW?
- What can I do with ClustalW?
- What type of sequences can ClustalW align?
- What input formats does ClustalW accept?
- What output formats does ClustalW produce?
- How can I save my alignment to a file?
- Is there a limit on the number of sequences or the size of the file that I submit to ClustalW?
- What do the file extensions mean that I get in my results?
- How are the pairwise alignment scores generated?
- How can I get the colour version of the alignment?
- Why can I not see the guide tree in my browser?
- What is Jalview?
- Why does Jalview not work for me?
- How can I save the guide tree image or the jalview alignment?
- What is the difference between a cladogram and a phylogram?
- Which method is used to draw the guide tree?
- Is there an alternative tree drawing program that can be used for large numbers of sequences?
- Is it possible to perform bootstrap analysis or to get the Bootstrap values along with the nodes of each branch of the phylogram?
- Can we have distance scale (as bar) based on the substitution rates along with the phylogram?
- What are the default parameters used by ClustalW?
- How can I see the parameter values that are used by the ClustalW program?
- How long are ClustalW results stored at the EBI?
- Does my job have an identifier?
- Where can I download the ClustalW software from?
- How do I reference use of this service?
- What is the difference between a guide tree and a true phylogenetic tree?
- Where can I find detailed information about ClustalW?
- How does Clustalw Work (very simple explanation)?
Why
use ClustalW?
Multiple alignments of protein sequences are important
tools in studying sequences. The basic information they provide is the
identification of conserved sequence regions. This is very useful in designing
experiments to test and modify the function of specific proteins, in predicting
the function and structure of proteins and in identifying new members of
protein families.
How
can I use ClustalW?
The ClustalW web form is available at http://www.ebi.ac.uk/clustalw/.
There are two ways to use this service at the EBI. The first is interactively
(default) and the second is by email. Using it interactively, the user must
wait for the results to be displayed in the browser window. The email option
means that the results will not be displayed in the browser window but will be
sent by email. The email option is the better one to take when submitting large
amounts of data.
ClustalW is also available from within SRS
(http://srs.ebi.ac.uk).
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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