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ClustalW
There is still one problem for ClustalW as for all other stand alone alignment programs. None of them can visualize annotations on the aligned sequences.
Most
researches align their own
sequence to some reference sequences which are often retrieved from one
or more of the large
public databases, eg GenBank. As input these programs require a Fasta
file and they typically
export in their own alignment format. The ClustalW plug-in for use in a
CLC Workbench use the
ClustalW program for the alignment calculation but still retains
annotations on the sequences
when the alignment is displayed.
One of the advantages of ClustalW is that it uses very little computer memory on rather large sequences so one is able to align large sequences without needing a state-of-the-art computer.
When you do a ClustalW alignment in a CLC Workbench, the
following parameters can be set:
- Extra command line options, making it possible to specify extra program specific command line options and advanced settings. The available commandline options are available thought the manual of the individual alignment methods.
- Custom gap open penalty. Set the gap opening costs.
- Custom gap extension penalty. Set the gap extension costs.
- Free end costs. Enable free end costs.
- Slow/accurate. Use a very accurate alignment method.
- Fast/approximate. Use a fast but less accurate alignment method.
- Scoring matrix. Select from a list of different scoring matrices.
Speed up ClustalW using CLC bio's high-performance computing solutions.
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