This dialog box displays a single tab containing a set of organized parameters that are used by ClustalW to align Protein sequences.
In this dialog box, you will see the following options:
Gap Opening Penalty: The penalty for opening a gap in the alignment. Increasing this value makes the gaps less frequent.
Gap Extension Penalty: The penalty for extending a gap by one residue. Increasing this value will make the gaps shorter. Terminal gaps are not penalized.
Gap Opening Penalty: The penalty for opening a gap in the alignment. Increasing this value makes the gaps less frequent.
Gap Extension Penalty: The penalty for extending a gap by one residue. Increasing this value will make the gaps shorter. Terminal gaps are not penalized.
Protein Weight Matrix: The scores assigned to matches and mismatches (including IUB ambiguity codes).
Residue-specific Penalties: Amino acid specific gap penalties that reduce or increase the gap opening penalties at each position or sequence in the alignment. For example, positions that are rich in glycine are more likely to have an adjacent gap than positions that are rich in valine. See the documentation for details.
Hydrophilic Penalties: Used to increase the chances of a gap within a run (5 or more residues) of hydrophilic amino acids; these are likely to be loop or random coil regions in which gaps are more common.
Gap Separation Distance: Tries to decrease the chances of gaps being too close to each other. Gaps that are less than this distance apart are penalized more than other gaps. This does not prevent close gaps; it makes them less frequent, promoting a block-like appearance of the alignment.
Use Negative Matrix: When enabled negative weight matrix values will be used if they are found; otherwise the matrix will be automatically adjusted to all positive values.
Delay Divergent Cutoff (%): Delays the alignment of the most distantly-related sequences until after the alignment of the most closely-related sequences. The setting shows the percent identity level required to delay the addition of a sequence; sequences that are less identical than this level will be aligned later.
Keep Predefined Gaps: When checked, any alignment positions in which ANY of the sequences have a gap will be ignored.
Specify Guide Tree: Browser for and select a guide tree (in Newick format) to be used for the alignment. If this option is not used, then a Neighbor-Join tree will be created and automatically used as the guide tree.
NOTE: All definitions are derived from CLUSTALW manual.