This dialog box displays a single tab containing a set of organized parameters that are used by ClustalW to align the DNA sequences. If you are aligning protein-coding sequences and have not used the Align by ClustalW (Codons) menu item, please note that CLUSTALW will not respect the codon positions and may insert alignment gaps within codons. For aligning cDNA or sequence data containing codons, we recommend that you align the translated protein sequences (see Aligning coding sequences via 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.
Common Parameters
DNA Weight Matrix: The scores assigned to matches and mismatches (including IUB ambiguity codes).
Transition Weight: Gives transitions a weight between 0 and 1. A weight of zero means that the transitions are scored as mismatches, while a weight of 1 gives the transitions the match score. For distantly-related DNA sequences, the weight should be near zero; for closely-related sequences, it can be useful to assign a higher score.
Use Negative Matrix: 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 most closely-related sequences have been aligned. The setting shows the percent identity level required to delay the addition of a sequence. Sequences that is less identical than this level will be aligned later.
Keep Predefined Gaps: When checked, 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 the CLUSTALW manual.