EMBOSS explorer

clustal

Global multiple alignment of sequences (read the manual)

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

Input section

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
Pairwise Alignment section
Algorithm for pairwise alignments
Nucleotide comparison matrix for pairwise alignment
Amino acid comparison matrix for pairwise alignment
User provided symbol comparison matrix (in BLAST format):
Gap penalty for pairwise alignment (default is 15.0 for nucleic, 10.0 for protein)
Gap length penalty for pairwise alignment (default is 6.66 for nucleic, 0.1 for protein)
K-tuple size (default is 2 for nucleic, 1 for protein)
Top Diagonals (default is 4 for nucleic, 5 for protein)
Window size (default is 4 for nucleic, 5 for protein)
Joining penalty (default is 5 for nucleic, 3 for protein)
Multiple Alignment section
Clustering method
Nucleotide comparison matrix for multiple alignment
Amino acid comparison matrix for multiple alignment
User provided symbol comparison matrix (in BLAST format):
Rescale amino acid comparison matrix to all positive values?
Transition weight
Gap penalty for multiple alignment (default is 15.0 for nucleic, 10.0 for protein)
Gap length penalty for multiple alignment (default is 6.66 for nucleic, 0.2 for protein)
Max. % identity for delay of divergent sequences
Use gap penalties dependent on amino acids at edge?
Use lower gap penalties in strings of at least 5 hydrophylic amino acids?
Hydrophylic amino acids
Gap Separation Distance
Do gap Separation at ends?
Iterative realignment of sequences
Maximum number of iterations
Weight sequences?
Output section
Order of sequences in output
Output sequence 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.