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April 19th, 2024: NPS@ updated (see NEWS).

A brief introduction to MUSCLE
MUSCLE 5 is a novel algorithm which constructs an ensemble of high-accuracy MSAs with diverse biases by perturbing a hidden Markov model and permuting its guide tree. Confidence in an inference is assessed as the fraction of the ensemble which supports it. Ensemble analysis can improve confidence assessment in any inference from an MSA.

Availability in NPS@
MUSCLE is available :

• for aligning protein sequences
• for aligning nucleotide sequences
• when you work with a set of sequences in NPS@ (if the set contains at least two sequences)

Parameters
The -super5 option is used for computation.
The output format is CLUSTAL W.

NPS@ MUSCLE output example
The NPS@ MUSCLE output is divided into three parts.

• PART 1:
  After the reference, you have buttons to post-process the multiple alignment with other software like HMMBUILD, Repertoire, ... In this part, you have also a form to work with the alignment. Your choices are validate when you click on the SHOW button. You can :
  • show residues with different options (identical(*), strongly similar (:), weakly similar (.), ...). The most interesting option is the "using conservation level" one. With it you, display only residues that have a conservation level equal or above the value you type in.
  • select secondary structure prediction methods to compute and display. This in the case of proteins and when you have no more than 50 sequences. A method with the "(Do it alone)" sentence has to be computed alone (it must be the only one newly selected before the next click on "SHOW" button). Otherwise, you won't have your response because of the timeout (these methods can take 5 minutes or more by sequence). You can also show all methods with or without secondary consensus or only the consensus. You can also see the percentage of each secondary structure element (HETC...) for each method.
  
  


• PART 2:
  It's the color coded alignment with or without secondary structure predictions inserted.
  
  


• PART 3:
  You have :
  • The percentage of each secondary structure element (if wanted) for each prediction and for each sequence.
  • Some data on the alignment (length, number of identities,...).
  • MUSCLE options used.
  • Links on result text files (MUSCLE, secondary structure prediction method outputs,...).
  • Secondary structure prediction method parameters choice.
  
  

References

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