These parameters control the final multiple alignment. This is the core of
the program and the details are complicated. To fully understand the use
of the parameters and the scoring system, you will have to refer to the
Each step in the final multiple alignment consists of aligning two alignments
or sequences. This is done progressively, following the branching order in
the GUIDE TREE. The basic parameters to control this are two gap penalties and
the scores for various identical/non-indentical residues.
1) and 2) The GAP PENALTIES are set by menu items 1 and 2. These control the
cost of opening up every new gap and the cost of every item in a gap.
Increasing the gap opening penalty will make gaps less frequent. Increasing
the gap extension penalty will make gaps shorter. Terminal gaps are not
3) The DELAY DIVERGENT SEQUENCES switch, 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 are less identical than this level
to any other sequences will be aligned later.
4) For DNA, the scoring system assigns a score of 3 for two identical bases
and zero otherwise. The TOGGLE TRANSITIONS switch (menu item 3) gives
transitions (A <--> G or C <--> T i.e. purine-purine or pyrimidine-pyrimidine
substitutions) a score of 1; otherwise, these are scored as mismatches and
get a score of zero. For distantly related DNA sequences, this switch
might be better turned off; for closely related sequences it can be useful.
5) and 6)PROTEIN WEIGHT MATRIX leads to a new menu where you are offered a
choice of weight matrices. The default is the BLOSUM series of
matrices by Jorja and Steven Henikoff. Note, a series is used! The actual
matrix that is used depends on how similar the sequences to be aligned at this
alignment step are. Different matrices work differently at each
evolutionary distance. Further help is offered
7)PROTEIN GAP parameters, see here