MUSCLE run mode Click here for details.:

Note: parameters are adjusted according to the selected running mode

Maximum number of iterationsYou can control the number of iterations that MUSCLE does. If you specify 1, 2 or 3, then this is exactly the number of iterations that will be performed. 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, curation may be rather slow.: (default: 16)
Find diagonalsCreating a pair-wise alignment by dynamic programming requires computing an L1 × L2 matrix, where L1 and L2 are the sequence lengths. A trick used in algorithms such as BLAST is to reduce the size of this matrix by using fast methods to find diagonals, i.e. short regions of high similarity between the two sequences. This speeds up the algorithm at the expense of some reduction in accuracy. MUSCLE uses a technique called k-mer extension to find diagonals. (faster for similar sequences)

For a less stringent selection: For a more stringent selection:

Statistical tests for branch support:
Approximate Likelihood-Ratio Test (aLRT):    SH-like Chi2-based parametric Minimum of SH-like and Chi2-based
Bootstrapping procedure:    Number of bootstraps:   

Number of substitution rate categories:
Gamma distribution parameter: estimated     fixed:    
Proportion of invariable sites: estimated     fixed:    
Transition / transversion ratio (nucleic acids only): estimated     fixed:    
Remove gaps from alignment    

Tree can be customized using the dynamic tree editing interface.