EMBOSS explorer

muscle

Multiple alignment of sequences by global optimization (read the manual)

Unshaded fields are optional and can safely be ignored. (hide optional fields)

Input section
Refine existing alignment?

Select an input sequence. Use one of the following three fields:

  1. To access a sequence from a database, enter the USA here:
  2. To upload a sequence from your local computer, select it here:
  3. To enter the sequence data manually, type here:
Use user provided guide tree?
User provided guide tree:
Additional section
Perform algorithm up to stage
Profile-profile alignment section
Scoring scheme for protein profile-profile alignment
User provided symbol comparison matrix (in BLAST format):
Gap opening penalty
Gap extension penalty
Minimum size hydrophobic region for increasing gap penalty
Multiplier for increasing gap penalty in hydrophobic region
Use diagonal optimization for k-mer clustering stage?
Use diagonal optimization for tree refinement stage?
Sequence weighting scheme for k-mer clustering and tree refinement stages
Sequence weighting scheme for bipartite refinement stage
Tree building section
Maximum number of iterations at tree refinement stage
Clustering method for k-mer clustering and tree refinement stages
Clustering method for bipartite refinement stage
Proportion between average linkage and minimum linkage for UPGMB
Distance measure for k-mer clustering stage
Distance measure for tree refinement and bipartite refinement stages
Global optimization section
Maximum number of iterations at bipartite refinement stage
Objective score for bipartite refinement
Anchor alignment?
Minimum spacing between anchors
Advanced section
Maximum number of hours to run
Output section
Order of sequences in output
Output sequence format
Write output file with guide tree from k-mer clustering in nested parentheses format?
Write output file with guide tree from tree refinement in nested parentheses format?
Run section
Email address: If you are submitting a long job and would like to be informed by email when it finishes, enter your email address here.