Alignments
BioloMICS:
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Minimum sequence size (8) Minimum size of a sequence.
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Minimum numerator (0) Minimum numerator (0).
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Single insertion penalty (0.5) Penalty for a single insertion.
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Double insertion penalty (0.7) Penalty for a double insertion.
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Mutation penalty (1.0) Penalty for a mutation.
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Precise Precise.
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Field algorithm Algorithms listed for different field types.
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Alignment algorithm Biolomics, Blast, Fasta or MultiAlign.
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Alignment method Logical, BestCase or ExactMatch.
Blast:
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Minimum similarity to keep results Minimum similarity to keep results.
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Minimum overlap to keep results Minimum overlap to keep results.
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Overlap rating reward Overlap rating reward.
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Gap creation penalty Penalty when creating a gap.
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Gap extension penalty Penalty when extending a gap.
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Maximum alignments to display Maximum number of alignments to display.
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Maximum allowed time per alignment Maximum allowed time per alignment.
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Minimum sequences length Minimum length of a sequence.
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Penalty mismatch Penalty for a mismatch.
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Reward match Reward for a match.
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Word size Length of the initial words. Default is 11, but can be decreased (to a minimum of 7) to increase the sensitivity. When increasing the word size, the search speed will be increased.
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Sequence type Blastn, Blastp, Blastx, TBlastn, TBlastx, Fastan or Fastap.
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Select sorting mode Rating, Similarity or Probability.
Multiple alignments:
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Strategy
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Automatic detection of the most appropriate algorithm
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Very fast progressive method with a rough guide tree
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Fast progressive method
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Accurate iterative method suitable for less than 200 sequences of similar length
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Most accurate iterative refinement method suitable for less than 200 sequences
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Accurate method suitable for less than 200 sequences containing large unalignable regions
Click Save to save the changes made and to close the Options dialog.
