new_calc : bool (default=True)
Specify, whether the analysis should be repeated from the
beginning, or whether already conducted analyses should be carried
out.
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
List2012b, and
- “asjp” – an independent sound-class model which is based on the
sound-class model of Brown2008 and the empirical data
of Brown2011 (see the description in
List2012.
mode : string (default=”global”)
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.
gop : int (default=-3)
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 Gotoh1982.
factor : float (default=1)
The factor by which the initial and the descending position shall
be modified.
tree_calc : { ‘neighbor’, ‘upgma’ }
The cluster algorithm which shall be used for the calculation of
the guide tree. Select between neighbor, the Neighbor-Joining
algorithm (Saitou1987), and upgma, the UPGMA
algorithm (Sokal1958).
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.
restricted_chars : string (default=”T”)
Define which characters of the prosodic string of a sequence
reflect its secondary structure (cf. List2012b) and
should therefore be aligned specifically. This defaults to “T”,
since this is the character that represents tones in the prosodic
strings of sequences.
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