threshold : float
The threshold for the flat cluster analysis.
check : string (default=”final”)
Specify when to check for improved sum-of-pairs scores: After each
iteration (“immediate”) or after all iterations have been carried
out (“final”).
mode : { ‘global’, ‘overlap’, ‘dialign’ }
A string indicating which kind of alignment analysis should be
carried out during the progressive phase. Select between:
- ‘global’ – traditional global alignment analysis based on the
Needleman-Wunsch algorithm Needleman1970,
- ‘dialign’ – global alignment analysis which seeks to maximize
local similarities Morgenstern1996.
- ‘overlap’ – semi-global alignment, where gaps introduced in the
beginning and the end of a sequence do not score.
gop : int (default=-5)
The gap opening penalty (GOP) used in the analysis.
gep_scale : float (default=0.6)
The factor by which the penalty for the extension of gaps (gap
extension penalty, GEP) shall be decreased. This approach is
essentially inspired by the exension of the basic alignment
algorithm for affine gap penalties [Goto81].
scale : tuple or list (default=(3,1,2))
The scaling factors for the modificaton of gap weights. The first
value corresponds to sites of ascending sonority, the second value
to sites of maximum sonority, and the third value corresponds to
sites of decreasing sonority.
factor : float (default=0.3)
The factor by which the initial and the descending position shall
be modified.
gap_weight : float (default=0)
The factor by which gaps in aligned columns contribute to the
calculation of the column score. When set to 0, gaps will be
ignored in the calculation. When set to 0.5, gaps will count half
as much as other characters.
|