├── README.md ├── kClust ├── kClust_mkAln └── src ├── Makefile ├── README ├── alignment.cpp ├── alignment.h ├── base_table.cpp ├── base_table.h ├── block_manager.cpp ├── block_manager.h ├── blosum100.out ├── blosum30.out ├── blosum35.out ├── blosum40.out ├── blosum45.out ├── blosum50.out ├── blosum55.out ├── blosum60.out ├── blosum62.out ├── blosum65.out ├── blosum70.out ├── blosum75.out ├── blosum80.out ├── blosum85.out ├── blosum90.out ├── blosum95.out ├── chronometer.cpp ├── chronometer.h ├── clusters.cpp ├── clusters.h ├── converter.cpp ├── converter.h ├── dummy_matrix.h ├── fasta_db_reader.cpp ├── fasta_db_reader.h ├── heap_wrapper.h ├── kClust.cpp ├── kClust_benchmarks.cpp ├── kClust_mkAln.cpp ├── kClust_mkAlnDB.cpp ├── kDP.cpp ├── k_clust.cpp ├── k_clust.h ├── kmer.cpp ├── kmer.h ├── kmer_matrix.cpp ├── kmer_matrix.h ├── kmer_seed_list.cpp ├── kmer_seed_list.h ├── kmeraln.cpp ├── kmeraln.h ├── matrix.cpp ├── matrix.h ├── mkaln.cpp ├── mkaln.h ├── mkaln_onlycons.cpp ├── mkaln_orig.cpp ├── my_exception.h ├── mysql_spec_structures.h ├── mysqldb.cpp ├── mysqldb.h ├── packed_sequence.cpp ├── packed_sequence.h ├── pair_aln.cpp ├── pair_aln.h ├── params.cpp ├── params.h ├── profile.cpp ├── profile.h ├── recycle_table.cpp ├── recycle_table.h ├── sequence.cpp ├── sequence.cpp~ ├── sequence.h ├── simple_hash.h ├── simple_list.h ├── swaln.cpp ├── swaln.h ├── test.cpp ├── wn1dmin.c ├── wnabs.h ├── wnasrt.c ├── wnasrt.h ├── wnbar.c ├── wnbar2.c ├── wnclone.cpp ├── wncmp.h ├── wncnjfg.c ├── wnconj.h ├── wnconjd.c ├── wnconjd.h ├── wnconjg.c ├── wncons.h ├── wncpy.h ├── wndcmp.c ├── wndot.c ├── wnerr.h ├── wnffln.c ├── wnffln.h ├── wnfft.h ├── wnlbfgs.c ├── wnlib.h ├── wnmat.h ├── wnmax.h ├── wnmbtr.c ├── wnmbtr.h ├── wnmecp.c ├── wnmem.c ├── wnmem.h ├── wnmemb.c ├── wnmemb.h ├── wnmemg.c ├── wnmemn.c ├── wnmemw.h ├── wnmmk.c ├── wnmqf.c ├── wnmqf.h ├── wnnlp.c ├── wnnlp.h ├── wnnmgd.c ├── wnnop.h ├── wnparvect.c ├── wnparvect.h ├── wnpen.c ├── wnpoly.c ├── 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