Helper Functions for SCA Alignment (calign, and misc)

The helper functions and classes below play an important role in all SCA alignment algorithms in LingPy (List2012b). They are implemented both in pure Python and in Cython (only supported for Python 3), in order to allow for faster implementations of the core alignment functions. Instead of using these functions directly, we recommend to use the more general functions which you can find in the pairwise and the multiple module of LingPy, and which are based on the helper functions we list below.

Functions

globalign Carry out global alignment of two sequences.
secondary_globalign Carry out global alignment of two sequences with secondary sequence structures.
localign Carry out semi-global alignment of two sequences.
secondary_localign Carry out lobal alignment of two sequences with sensitivity to secondary sequence structures.
semi_globalign Carry out semi-global alignment of two sequences.
secondary_semi_globalign Carry out semi-global alignment of two sequences with sensitivity to secondary sequence structures.
dialign Carry out dialign alignment of two sequences.
secondary_dialign Carry out dialign alignment of two sequences with sensitivity for secondary sequence structures.
align_pair Align a pair of sequences.
align_pairwise Align a list of sequences pairwise.
align_pairs Align multiple sequence pairs.
align_profile Align two profiles using the basic modes.
score_profile Basic function for the scoring of profiles.
swap_score_profile Basic function for the scoring of profiles which contain swapped sequences.
corrdist Create a correspondence distribution for a given language pair.

Classes

ScoreDict Class allows quick access to scoring functions using dictionary syntax.