High-Performance Computing at the NIH
Multiple Alignment Workshop (MAW)
Calculate & compare a multiple sequence alignment using one or more selected algorithms
 Help

Input Sequences DNA or Protein sequences in Fasta, GenBank, EMBL, Swiss-Prot, or Clustalw format.

Upload local file
or  
Enter text
or  
Load example  
Alignment Methods   

clustal  select options msa      select options muscle   select options probcons select options dialign  select options poa      select options tcoffee  select options

 

 

 

clustal Options
Pairwise Alignment
Slow Accurate
Gap opening penalty [0-100]:
-pwgapopen 
Gap Extension Penalty [0-100]:
-pwgapext 
DNA weight matrix:
-pwdnamatrix 
Protein comparison matrix:
-pwmatrix 
(-quicktree) Fast Approximate
Gap Penalty [0-500]:
-pairgap 
Number of top diagonals (1 to 4000):
-topdiags 
Window size (1 to 50):
-window 
K-tuple:
-ktuple 
Multiple Alignment
Gap opening penalty [0-100]:
-gapopen 
Delay divergent sequences:
-maxdiv %
DNA weight matrix:
-dnamatrix 
Protein comparison matrix:
-matrix 
Gap Extension Penalty [0-100]:
-gapext 
Negative matrix:
-negative    off 
Transition weight (DNA)(0-1):
-transweight 
 
 
Protein Gap
Residue-specific penalties:
-nogap    on 
Hydrophilic residues:
-hgapresidues 
Gap separation distance[0-100]:
-gapdist 
Hydrophilic penalties:
-nohgap    on 
End gap separation penalty:
-endgaps    off 
 
 

dialign Options
Diagonal threshhold: -thr
Iterative scoring: -it   off
Overlap weights: -ow (always)    (#seq<35)   -iw (never)
Clustering method: -max_link   -min_link   UPGMA
Asterisk mask: -mask   off
Maximum fragment length: -lmax
Minimum similarity value: -smin

msa Options
Terminal gap charge: -g (same as internal gaps)   no charge
Alignment cost: -b (unweighted sum)   weights by rationale-2
Maximal score: -d

muscle Options
Maximum iteration: -maxiters
Diagonal optimization: -diags   off

poa Options
Aggressive fusion: -fuseall   off  
Heavy bundling: -hb   off    -hbmin %
Alignment: -do_global   off    -do_progressive   off

probcons Options
Consistency: -c [0-5]
Iterative refinement: -ir   off
Pre-training: -pre   off
Viterbi coding: -viterbi   off

tcoffee Options
Gap penalties: -gapopen       -gapext       -cosmetic_penalty 
Terminal gaps: -tgmode 
Dynamic programming: -dp_mode 
Normalize scoring: -do_normalise       -ndiag       -diag_mode 

Output Formats  (shading details)

Shading: Consensus shaded by identity   by similarity  
show conserved   reverse
  Protein colored  
Ordering: as input    as aligned  

Comments/problems to webtools@helix.nih.gov
Helix Systems | Contact Helix | Search | Sitemap
Disclaimer | Privacy | Accessibility | CIT | NIH | DHHS | USA.gov