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Muscle

Information about the program:

Multiple DNA and protein sequence alignment.

How to use:

To input the data, copy them to the clipboard and paste into the text input field. To do so, press the Ctrl-Ins or Ctrl-V key combination. After this, the data located in the field, will be brought up as text. After data input in field, to launch the program, click the "Submit" button. After this, the server will accept a file as a computational task. To launch the control example, go to the launch panel for the control examples and go to one of the links in the panel. To obtain information about the program go to the "Help" link.

After execution, the results window will appear in the left panel. This page has 3 links to the different ways, the viewer can display the calculation results. A new browser window, which displays on the screen the initial set of sequences in text format, may be brought up by pressing the "Sequences under analysis" link. Pressing the "Multiple sequence alignment in FASTA format" link, you get a new browser window, which shows up the multiple sequence alignment in FASTA format. Pressing to the "Return to the program" link, the user can go to the start page. Choosing "Colored multiple sequence alignment", the user get a new browser window, which shows up the multiple sequence alignment in HTML format.

Algorithm:

MUSCLE algorithm (multiple sequence alignment by log-expectation) improves on progressive methods with a more accurate distance measure to assess the relatedness of two sequences. The distance measure is updated between iteration stages. [Edgar, R.C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.]

Input data:

Protein or DNA sequences in FASTA format

Output data:

Multiple sequence alignment in FASTA format