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Martinsos / edlib

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
http://martinsos.github.io/edlib
MIT License
493 stars 162 forks source link

Edlib for 1 vs N or N vs N #118

Open Martinsos opened 6 years ago

Martinsos commented 6 years ago

Edlib does pairwise (1 vs 1) alignment, and while it can also be used for 1 vs N or N vs N that way, it would be interesting to see if implementing direct support for 1 vs N or N vs N in it could offer some speedups, maybe by reusing some resources or smt hm. I think here it is important to understand such use cases.

Martinsos commented 6 years ago

Actually #113 is connected to this.

Martinsos commented 3 years ago

In https://github.com/Martinsos/edlib/issues/157, use case for this is also mentioned.

Easiest way to approach for this would be to optimize 1 vs N scenario and reuse, for example, Peq table, and maybe something more.