| Substitution Matrix or Scores |
Substitution Matrix
Scores
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Specify, whether you want to provide a substitution matrix for the scores, or provide the match and mismatch scores with the options '-r' and '-q'.
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Substitution Matrix
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Upload or enter a matrix. Details on the required format are
given in the usage section. If you upload or enter a
substitution matrix, you cannot define the match score and
mismatch cost.
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| Match Score (-r) |
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By default, this pipeline uses a match score of 6 for
"Dengue virus serotype classification".
For "Plasmodium polymorphisms", the match score is defined
by a specific substitution matrix (4 for A/T, 9 for C/G).
The LAST default match score is 6.
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| Mismatch Cost (-q) |
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By default, this pipeline uses a mismatch cost of 12 for
"Plasmodium polymorphisms" and for "Dengue virus serotype
classification". The LAST default mismatch cost is 18.
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| Gap Existence Cost (-a) |
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By default, this pipeline uses a gap existence cost of 12
for "Plasmodium polymorphisms" and for "Dengue virus serotype
classification". The LAST default gap existence cost is 21.
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| Gap Extension Cost (-b) |
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By default, this pipeline uses a gap extension cost of 3 for
"Plasmodium polymorphisms" and 4 for "Dengue virus serotype
classification". The LAST default gap extension cost is 9.
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| Insertion Existence Cost (-A) |
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By default, this pipeline uses a insertion existence cost of 15
for "Plasmodium polymorphisms" and for "Dengue virus serotype
classification". By default, the LAST insertion existence cost
is set to the same value as the gap existence cost (-a).
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| Query Letters per Random Alignment (-D) |
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By this option you can specify to report alignments that are
expected by chance at most once per x (-D) query letters.
By default, this pipeline uses a value of 1e+07 for "Plasmodium
polymorphisms" and for "Dengue virus serotype classification".
The default value used by LAST is 1e+06.
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