Score Matrix: Pair alignments will use the score matrix that is selected here. See the Score Matrix section of general Bonsai help for information on score matrices and appropriate matrix choice. For proteins, the Bonsai default is to use an adaptive score matrix, meaning that it will attempt to choose a matrix that is best suited for the particular pair alignment. For DNA, the default is a matrix based on the Kimura model of DNA evolution. If you choose a particular score matrix from the pop-up list, it will override the adaptive method.
Gap Open and Gap Extend Penalties: You can select gap penalties from a list of reasonable alternatives. Typically, a gap open penalty of 8 to 12 and a gap extend penalty of 1 or 2 are good choices. The gap open penalty is the cost of starting an alignment indel, and the extend penalty is the cost for each additional residue added to the indel. The extend penalty is usually much lower because indels tend to arise in specific sequence positions that tolerate them, the appearance of an indel of any size is a predictor that a larger indel is tolerable.
Allow Local Alignment: The default setting for pair alignments is to do a full-length alignment. You can change this to show only the best local alignment by checking this box. The best local aligned region should always be found somewhere within the full-length alignment. For sequences that have reasonable similarity across their entire length, these two settings will produce very similar results, with perhaps a few extra amino acids on each end for the full length alignment. Try both and see.
Display checkboxes: Check the display types that you would like this Pair Alignment to produce. Any combination can be displayed. Some other displays can be generated after the alignment.
Click "Close" (or use the window close icon) to close the settings frame. All changes made in this panel are effective immediately, so you won't lose your changes.
Click "View Score Matrix" to view the currently selected substitution score matrix in full.
Click "Set Defaults" to restore all of the default settings for the current type of pair alignment (protein or DNA).
[Possible additions: suboptimal alignment display, secondary structure prediction]