1) RESIDUE SPECIFIC PENALTIES are amino acid specific gap penalties that reduce
or increase the gap opening penalties at each position in the alignment or
sequence. See the documentation for details. As an example, positions that
are rich in glycine are more likely to have an adjacent gap than positions that
are rich in valine.
2) 3) HYDROPHILIC GAP PENALTIES are 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 where gaps are more common. The residues that
are "considered" to be hydrophilic are set by menu item 3.
4) 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 penalised more than other gaps. This does not prevent close gaps;
it makes them less frequent, promoting a block-like appearance of the alignment.
5) END GAP SEPARATION treats end gaps just like internal gaps for the purposes
of avoiding gaps that are too close (set by GAP SEPARATION DISTANCE above).
If you turn this off, end gaps will be ignored for this purpose. This is
useful when you wish to align fragments where the end gaps are not biologically