High-Performance Computing at the NIH

Multiple Alignment Workshop (MAW)
Calculate & compare a multiple sequence alignment using one or more selected algorithms
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Input Sequences DNA or Protein sequences in Fasta, GenBank, EMBL, Swiss-Prot, or Clustalw format.

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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  


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