model : string (default=”sca”)
A string indicating the name of the
Model object that shall be used for
the analysis.
Currently, three models are supported:
- “dolgo” – a sound-class model based on Dolgopolsky1986,
- “sca” – an extension of the “dolgo” sound-class model based on
List2012a, and
- “asjp” – an independent sound-class model which is based on the
sound-class model of Brown2008 and the empirical data of
Brown2011.
mode : string (default=”global”)
A string indicating which kind of alignment analysis should be
carried out. Select between:
- “global” – traditional global alignment analysis based on the
Needleman-Wunsch algorithm Needleman1971,
- “local” – local alignment analysis based on the Smith-Waterman
algorithm Smith1981,
- “overlap” – overlap alignment analysis where gaps introduced in
the beginning or the end of the alignment are scored with 0.
- “dialign” – global alignment analysis which seeks to maximize
local similarities Morgenstern1996.
gop : int (default=-5)
The gap opening penalty (gop) on which the analysis shall be based.
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 Gotoh1982.
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.
restricted_chars : string (default=”T”)
Define which characters of the prosodic string of a sequence
reflect its secondary structure (cf. List2012a) and
should therefore be aligned specifically. This defaults to “T”,
since this is the character that represents tones in the prosodic
strings of sequences.
|