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We have implemented our algorithm in C++. Currently it is using own input and output formats. You can download source code of our implementation (the license is GPLv3). We have implemented HERD in C++ and it heavily use templates so if you have less than 350MB of free memory, you may have problems to compile it (at least with gcc).

Note: There will be an new version of HERD soon (cleanup of code, new features and ability to read FASTA input files).