Martinsos / edlib

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
http://martinsos.github.io/edlib
MIT License
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Compare with some other aligning method (maybe SSW?). Test on nucleotide data. #1

Closed Martinsos closed 10 years ago

Martinsos commented 10 years ago

Tests performed! I compared Myers to SSW. In some scenarios Myers is faster, although not doing exactly the same thing. When aligning read to sequence, HW is appropriate, however it is as fast as SSW. When comparing two proteins, NW is appropriate, and it is much faster then SSW. When searching for best prefix, SHW is appopriate, and SSW does not offer anything for that (because it has only SW).