LingPy

This documentation is for version 2.0.dev, which is not released yet.

lingpy.align.multiple.mult_align

lingpy.align.multiple.mult_align(seqs, gop=-1, scale=0.5, tree_calc='upgma', pprint=False)

A short-cut method for multiple alignment analyses.

Parameters :

seqs : list

The input sequences.

gop = int (default=-1) :

The gap opening penalty.

scale : float (default=0.5)

The scaling factor by which penalties for gap extensions are decreased.

tree_calc : { “upgma” “neighbor” } (default=”upgma”)

The algorithm which is used for the calculation of the guide tree.

pprint : bool (default=False)

Indicate whether results shall be printed onto screen.

Returns :

alignments : list

A two-dimensional list in which alignments are represented as a list of tokens.

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