Helper Functions for Traditional Alignment (talign)

The helper functions and classes below play an important role in traditional alignment algorithms in LingPy which do not make use of sound classes. 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.
localign Carry out semi-global alignment of two sequences.
semi_globalign Carry out semi-global alignment of two sequences.
dialign Carry out dialign alignment of two sequences.
align_pair Align a pair of sequences.
align_pairwise Align all 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 in swapped sequences.