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| ***General settings:*** |
-quicktree
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Use FAST algorithm for the alignment guide tree
|
-type
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-negative
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Protein alignment with negative values in matrix
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| ***Fast Pairwise settings:**** |
-ktuple
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|
Word size
|
-topdiags
|
|
Number of best diags.
|
-window
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Window around best diags.
|
-pairgap
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|
Gap penalty
|
-score
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|
PERCENT or ABSOLUTE
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***Slow Pairwise settings:****
|
-pwmatrix
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|
Protein weight matrix
or
|
-pwdnamat
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|
DNA weight matrix
or
|
-pwgapopen
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|
Gap opening penalty(f)
|
-pwgapext
|
|
Gap extension penalty(f)
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***Multiple Alignments:***
|
-newtree
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|
File for new guide tree
|
-usetree
|
|
File for old guide tree
|
-matrix
|
|
Protein weight matrix
or
|
-dnamatrix
|
|
DNA weight matrix
or
|
-gapopen
|
|
Gap opening penalty(f)
|
-gapext
|
|
Gap extension penalty(f)
|
-endgaps
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|
No end gap separation pen.
|
-gapdist
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Gap separation pen. range
|
-nopgap
|
|
Residue-specific gaps off
|
-nohgap
|
|
Hydrophilic gaps off
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-hgapres
|
|
List hydrophilic res.
|
-maxdiv
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|
% ident. for delay
|
-transwet
|
|
Transitions weighting(f)
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