Installed MUSCLE

We have currently installed version 3.5 of the MUSCLE.
The reference for this tool is:

Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.

The official MUSCLE man page is available at this link.

Help for the Bioinformatica MUSCLE

Explanations for all the form options:

1. Choose a sequence type
• Muscle knows DNA and proteins, but you should not mix them in the same input file.
2. Type of alignment
• Standard alignments: The default settings are designed to give the best accuracy, so this may be all you need to know.
• Large alignments: If you have a large number of sequences (a few thousand), or they are very long, then the default settings of may be too slow for practical use. A good compromise between speed and accuracy is to run just the first two iterations of the algorithm. On average, this gives accuracy equal to T-Coffee and speeds much faster than CLUSTALW.
• Fastest speed: If you want the fastest possible speed,
• Huge alignments: If you have a very large number of sequences (several thousand), or they are very long, then the kbit20_3 option may cause problems because it needs a relatively large amount of memory.
3. Iterations
• controls the number of iterations that muscle will run. If the value is greater than 3, then muscle will continue up to the maximum you specify or until convergence is reached, which ever happens sooner. The default is 16. If you have a large number of sequences, refinement may be rather slow.
4. Tree
• This option controls the maximum number of new trees to create in iteration 2. Our experience suggests that a point of diminishing returns is typically reached after the first tree, so the default value is 1. If a larger value is given, the process will repeat until convergence or until this number of trees has been created, which ever comes first.
5. Output Format
• Default format is the Muscle format, with the alignment coloured. This format is always present.
  
• ClustalW: output as ClustalW program.
• PHYLIP1, PHYLIP2: Save tree produced in first or second iteration to given file in Newick (Phylip-compatible) format.
6. Sequences order in alignment
• Preserve input order of sequences in output file. Default is to group sequences by similarity.
7. Create Score File
• Output the score file
  
8. Sequence
• You can cut and paste or type nucleotide or protein sequences into the text window. The only accepted format is a FASTA format. This format contains a one line header followed by lines of sequence data. The first line starts with a " >" symbol and is followed by the name of the sequence. The rest of the line is a description of the sequence (optional). The sequence itself is written in the remaining lines. Blanks lines , spaces are ignored.
  
• All sequences must follow the IUB/IUPAC standard codes
• All sequences will be checked before running Blast, and errors will be pointed. Please correct them before resubmitting the sequence.

And run Muscle ! The next page will show a small alert window, which will provide you with a JobId. If you know the job will take a long time to execute, you can save this JobId (copy it), click on the exit button, and come back later to view the Muscle results on the web