EMBOSS explorer

kclustalw

Multiple sequence alignment using ClustalW 2 (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:
Advanced section
method used for pairwise alignment stage
Alignment output format. Values: 'aln1', 'aln2', 'gcg', 'phylip', 'pir' or 'gde'
protein scoring matrix
order of sequences in the alignment
word size
window size around best diagonals
gap creation penalty
gap extension penalty
gap separation penalty
Do not score end gaps?
Gap penalty
Top diagonals to consider
score type
Discard gap regions when calculating tree?
Use Kimura's correction?
Tree format. Values: 'none', 'nj', 'phylip' or 'dist'
Generate phylogenetic tree?
Perform 'fast' alignment?
Perform alignment?
Tree type. Values: 'nj' or 'upgmp'
Number of iterations
Iteration type. Values: 'none', 'alignment' or 'tree'
Output section
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.