| ktuple - Word Size |
This is the size of exactly matching fragment that is
used for pairwise alignment. Increase for speed; decrease for sensitivity.
For longer sequences (e.g. >1000 residues) you may need to increase the
default. |
| Window |
This is the number of diagonals around each of the 'best'
diagonals that will be used. Decrease for speed; increase for
sensitivity. |
| Top Diagonals |
The number of k-tuple matches on each diagonal (in an
imaginary dot-matrix plot) is calculated. Only the best ones (with most matches) are
used in the alignment. This parameter specifies how many. Decrease for speed;
increase for sensitivity. |
| Gap Penalty |
This is a penalty for each gap in the fast alignments. It
has little affect on the speed or sensitivity except for extreme
values. |
| Gap Open |
Gap opening penalty is the cost of opening up every new
gap. Increasing the gap opening penalty will make gaps less frequent. Terminal gaps
are not penalised. |
| Gap Extension |
Gap extension penalty is the cost of every item in a gap.
Increasing the gap extension penalty will make gaps shorter. Terminal gaps are not
penalised. |
| Gap Open |
The gap opening penalty is the cost of opening up every new
gap. Increasing the gap opening penalty will make gaps less frequent. Terminal gaps
are not penalised. |
| Gap Extension |
The gap extension penalty is the cost of every item in a gap.
Increasing the gap extension penalty will make gaps shorter. Terminal gaps are not
penalised. |
| Gap Distance |
The 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. |
| End Gap Penalty |
The 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).
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 meaningful. |
| Number of Iterations |
Number of iteartion steps if an iteration method was selected. |
| Alignment type |
The alignment method used to perform the pairwise alignments used to generate the guide tree. Option 'Fast' is faster than option 'Slow', but also less accurate. |
| Score type |
Fast pairwise alignment score type to output. You have the choice
between percent or absolute. |
| Protein Weight Matrix |
The selection of the weigth matrix can influence the alignment quality and result. |
| DNA Weight Matrix |
The selection of weigth matrix can influence the alignment quality and result. |
| Protein Weight Matrix |
The selection of the weigth matrix can influence the alignment quality and result. |
| DNA Weight Matrix |
The selection of weigth matrix can influence the alignment quality and result. |
| Iteration |
A remove first iteration scheme has been added. This can be used to improve the final
alignment or improve the alignment at each stage of the progressive alignment. During the
iteration step each sequence is removed in turn and realigned. If the resulting alignment
is better than the previous alignment it is kept. This process is repeated until the score
converges (the score is not improved) or until the maximum number of iterations is
reached. The user can iterate at each step of the progressive alignment by setting the
iteration parameter to TREE or just on the final alignment by seting the iteration
parameter to ALIGNMENT. The default is no iteration. The maximum number of iterations can
be set using the numiter parameter. |
| Clustering Type |
The type of clustering that is used. |
