LCSk++
LCSk++ is a similarity metric for long strings introduced in [1].
This is an implementation of a fast algorithm [2] for computing it.
How to use
First, build the project using make. For that you'll need C++11 compatible
compiler. Then use ./main or ./main_fasta executables. Both of them read
two strings from given files and output their LCSk++ to a file. Only difference
is that the first one takes raw text files while the second one takes files in FASTA
format. Running them with no arguments will give you more details on how to use
them.
Using it in your own project
Files you are going to need to include in your project are:
- lcskpp.cpp
- lcskpp.h
- utils.h
Only one method is exposed, and it's given in lcskpp.h.
Testing
See test/README.md.
References
[1] Filip Pavetic, Goran Zuzic, Mile Sikic: LCSk++: Practical similarity metric for long strings, http://arxiv.org/abs/1407.2407
[2] Filip Pavetic, Ivan Katanic, Gustav Matula, Goran Zuzic, Mile Sikic: Fast and simple algorithms for computing both LCSk and LCSk+, https://arxiv.org/abs/1705.07279