3894 lines
199 KiB
Text
3894 lines
199 KiB
Text
bin/blast_formatter
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bin/blastdb_aliastool
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bin/blastdbcheck
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bin/blastdbcmd
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bin/blastdbcp
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bin/blastn
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bin/blastp
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bin/blastx
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bin/convert2blastmask
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bin/datatool
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bin/deltablast
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bin/dustmasker
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bin/gene_info_reader
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bin/legacy_blast.pl
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bin/makeblastdb
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bin/makembindex
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bin/makeprofiledb
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bin/project_tree_builder
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bin/psiblast
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bin/rpsblast
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bin/rpstblastn
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bin/seedtop
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bin/segmasker
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bin/seqdb_demo
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bin/seqdb_perf
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bin/tblastn
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bin/tblastx
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bin/update_blastdb.pl
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bin/windowmasker
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bin/windowmasker_2.2.22_adapter.py
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include/ncbi-tools++/algo/blast/api/bl2seq.hpp
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include/ncbi-tools++/algo/blast/api/blast_advprot_options.hpp
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include/ncbi-tools++/algo/blast/api/blast_aux.hpp
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include/ncbi-tools++/algo/blast/api/blast_dbindex.hpp
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include/ncbi-tools++/algo/blast/api/blast_exception.hpp
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include/ncbi-tools++/algo/blast/api/blast_mtlock.hpp
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include/ncbi-tools++/algo/blast/api/blast_nucl_options.hpp
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include/ncbi-tools++/algo/blast/api/blast_options.hpp
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include/ncbi-tools++/algo/blast/api/blast_options_builder.hpp
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include/ncbi-tools++/algo/blast/api/blast_options_handle.hpp
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include/ncbi-tools++/algo/blast/api/blast_prot_options.hpp
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include/ncbi-tools++/algo/blast/api/blast_results.hpp
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include/ncbi-tools++/algo/blast/api/blast_rps_options.hpp
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include/ncbi-tools++/algo/blast/api/blast_seqinfosrc.hpp
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include/ncbi-tools++/algo/blast/api/blast_seqinfosrc_aux.hpp
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include/ncbi-tools++/algo/blast/api/blast_types.hpp
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include/ncbi-tools++/algo/blast/api/blastx_options.hpp
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include/ncbi-tools++/algo/blast/api/cdd_pssm_input.hpp
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include/ncbi-tools++/algo/blast/api/deltablast.hpp
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include/ncbi-tools++/algo/blast/api/deltablast_options.hpp
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include/ncbi-tools++/algo/blast/api/disc_nucl_options.hpp
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include/ncbi-tools++/algo/blast/api/effsearchspace_calc.hpp
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include/ncbi-tools++/algo/blast/api/hspstream_queue.hpp
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include/ncbi-tools++/algo/blast/api/local_blast.hpp
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include/ncbi-tools++/algo/blast/api/local_db_adapter.hpp
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include/ncbi-tools++/algo/blast/api/local_search.hpp
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include/ncbi-tools++/algo/blast/api/msa_pssm_input.hpp
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include/ncbi-tools++/algo/blast/api/objmgr_query_data.hpp
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include/ncbi-tools++/algo/blast/api/objmgrfree_query_data.hpp
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include/ncbi-tools++/algo/blast/api/phiblast_nucl_options.hpp
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include/ncbi-tools++/algo/blast/api/phiblast_prot_options.hpp
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include/ncbi-tools++/algo/blast/api/prelim_stage.hpp
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include/ncbi-tools++/algo/blast/api/psi_pssm_input.hpp
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include/ncbi-tools++/algo/blast/api/psibl2seq.hpp
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include/ncbi-tools++/algo/blast/api/psiblast.hpp
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include/ncbi-tools++/algo/blast/api/psiblast_iteration.hpp
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include/ncbi-tools++/algo/blast/api/psiblast_options.hpp
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include/ncbi-tools++/algo/blast/api/pssm_engine.hpp
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include/ncbi-tools++/algo/blast/api/pssm_input.hpp
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include/ncbi-tools++/algo/blast/api/query_data.hpp
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include/ncbi-tools++/algo/blast/api/remote_blast.hpp
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include/ncbi-tools++/algo/blast/api/remote_search.hpp
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include/ncbi-tools++/algo/blast/api/repeats_filter.hpp
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include/ncbi-tools++/algo/blast/api/rps_aux.hpp
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include/ncbi-tools++/algo/blast/api/rpsblast_local.hpp
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include/ncbi-tools++/algo/blast/api/rpstblastn_options.hpp
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include/ncbi-tools++/algo/blast/api/search_strategy.hpp
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include/ncbi-tools++/algo/blast/api/seedtop.hpp
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include/ncbi-tools++/algo/blast/api/seqinfosrc_seqdb.hpp
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include/ncbi-tools++/algo/blast/api/seqinfosrc_seqvec.hpp
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include/ncbi-tools++/algo/blast/api/seqsrc_multiseq.hpp
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include/ncbi-tools++/algo/blast/api/seqsrc_seqdb.hpp
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include/ncbi-tools++/algo/blast/api/setup_factory.hpp
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include/ncbi-tools++/algo/blast/api/sseqloc.hpp
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include/ncbi-tools++/algo/blast/api/subj_ranges_set.hpp
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include/ncbi-tools++/algo/blast/api/tblastn_options.hpp
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include/ncbi-tools++/algo/blast/api/tblastx_options.hpp
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include/ncbi-tools++/algo/blast/api/traceback_stage.hpp
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include/ncbi-tools++/algo/blast/api/uniform_search.hpp
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include/ncbi-tools++/algo/blast/api/version.hpp
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include/ncbi-tools++/algo/blast/api/windowmask_filter.hpp
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include/ncbi-tools++/algo/blast/blastinput/blast_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/blast_fasta_input.hpp
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include/ncbi-tools++/algo/blast/blastinput/blast_input.hpp
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include/ncbi-tools++/algo/blast/blastinput/blast_input_aux.hpp
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include/ncbi-tools++/algo/blast/blastinput/blast_scope_src.hpp
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include/ncbi-tools++/algo/blast/blastinput/blastn_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/blastp_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/blastx_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/cmdline_flags.hpp
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include/ncbi-tools++/algo/blast/blastinput/deltablast_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/igblastn_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/igblastp_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/psiblast_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/rmblastn_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/rpsblast_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/rpstblastn_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/tblastn_args.hpp
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include/ncbi-tools++/algo/blast/blastinput/tblastx_args.hpp
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include/ncbi-tools++/algo/blast/composition_adjustment/compo_heap.h
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include/ncbi-tools++/algo/blast/composition_adjustment/compo_mode_condition.h
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include/ncbi-tools++/algo/blast/composition_adjustment/composition_adjustment.h
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include/ncbi-tools++/algo/blast/composition_adjustment/composition_constants.h
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include/ncbi-tools++/algo/blast/composition_adjustment/matrix_frequency_data.h
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include/ncbi-tools++/algo/blast/composition_adjustment/nlm_linear_algebra.h
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include/ncbi-tools++/algo/blast/composition_adjustment/optimize_target_freq.h
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include/ncbi-tools++/algo/blast/composition_adjustment/redo_alignment.h
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include/ncbi-tools++/algo/blast/composition_adjustment/smith_waterman.h
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include/ncbi-tools++/algo/blast/composition_adjustment/unified_pvalues.h
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include/ncbi-tools++/algo/blast/core/aa_ungapped.h
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include/ncbi-tools++/algo/blast/core/blast_aalookup.h
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include/ncbi-tools++/algo/blast/core/blast_aascan.h
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include/ncbi-tools++/algo/blast/core/blast_def.h
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include/ncbi-tools++/algo/blast/core/blast_diagnostics.h
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include/ncbi-tools++/algo/blast/core/blast_encoding.h
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include/ncbi-tools++/algo/blast/core/blast_engine.h
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include/ncbi-tools++/algo/blast/core/blast_export.h
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include/ncbi-tools++/algo/blast/core/blast_extend.h
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include/ncbi-tools++/algo/blast/core/blast_filter.h
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include/ncbi-tools++/algo/blast/core/blast_gapalign.h
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include/ncbi-tools++/algo/blast/core/blast_hits.h
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include/ncbi-tools++/algo/blast/core/blast_hspfilter.h
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include/ncbi-tools++/algo/blast/core/blast_hspstream.h
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include/ncbi-tools++/algo/blast/core/blast_kappa.h
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include/ncbi-tools++/algo/blast/core/blast_lookup.h
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include/ncbi-tools++/algo/blast/core/blast_message.h
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include/ncbi-tools++/algo/blast/core/blast_nalookup.h
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include/ncbi-tools++/algo/blast/core/blast_nascan.h
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include/ncbi-tools++/algo/blast/core/blast_options.h
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include/ncbi-tools++/algo/blast/core/blast_parameters.h
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include/ncbi-tools++/algo/blast/core/blast_program.h
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include/ncbi-tools++/algo/blast/core/blast_psi.h
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include/ncbi-tools++/algo/blast/core/blast_query_info.h
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include/ncbi-tools++/algo/blast/core/blast_rps.h
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include/ncbi-tools++/algo/blast/core/blast_seg.h
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include/ncbi-tools++/algo/blast/core/blast_seqsrc.h
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include/ncbi-tools++/algo/blast/core/blast_seqsrc_impl.h
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include/ncbi-tools++/algo/blast/core/blast_setup.h
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include/ncbi-tools++/algo/blast/core/blast_stat.h
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include/ncbi-tools++/algo/blast/core/blast_sw.h
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include/ncbi-tools++/algo/blast/core/blast_toolkit.h
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include/ncbi-tools++/algo/blast/core/blast_traceback.h
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include/ncbi-tools++/algo/blast/core/blast_tune.h
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include/ncbi-tools++/algo/blast/core/blast_util.h
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include/ncbi-tools++/algo/blast/core/gapinfo.h
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include/ncbi-tools++/algo/blast/core/gencode_singleton.h
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include/ncbi-tools++/algo/blast/core/greedy_align.h
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include/ncbi-tools++/algo/blast/core/hspfilter_besthit.h
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include/ncbi-tools++/algo/blast/core/hspfilter_collector.h
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include/ncbi-tools++/algo/blast/core/hspfilter_culling.h
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include/ncbi-tools++/algo/blast/core/link_hsps.h
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include/ncbi-tools++/algo/blast/core/lookup_util.h
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include/ncbi-tools++/algo/blast/core/lookup_wrap.h
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include/ncbi-tools++/algo/blast/core/mb_indexed_lookup.h
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include/ncbi-tools++/algo/blast/core/na_ungapped.h
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include/ncbi-tools++/algo/blast/core/ncbi_math.h
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include/ncbi-tools++/algo/blast/core/ncbi_std.h
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include/ncbi-tools++/algo/blast/core/pattern.h
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include/ncbi-tools++/algo/blast/core/phi_extend.h
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include/ncbi-tools++/algo/blast/core/phi_gapalign.h
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include/ncbi-tools++/algo/blast/core/phi_lookup.h
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include/ncbi-tools++/algo/blast/core/split_query.h
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include/ncbi-tools++/algo/blast/dbindex/dbindex.hpp
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include/ncbi-tools++/algo/blast/dbindex/dbindex_sp.hpp
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include/ncbi-tools++/algo/blast/dbindex/sequence_istream.hpp
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include/ncbi-tools++/algo/blast/dbindex/sequence_istream_bdb.hpp
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include/ncbi-tools++/algo/blast/dbindex/sequence_istream_fasta.hpp
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include/ncbi-tools++/algo/blast/format/blast_format.hpp
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include/ncbi-tools++/algo/blast/format/blastfmtutil.hpp
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include/ncbi-tools++/algo/blast/format/blastxml2_format.hpp
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include/ncbi-tools++/algo/blast/format/blastxml_format.hpp
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include/ncbi-tools++/algo/blast/format/build_archive.hpp
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include/ncbi-tools++/algo/blast/format/data4xml2format.hpp
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include/ncbi-tools++/algo/blast/format/data4xmlformat.hpp
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include/ncbi-tools++/algo/blast/format/vecscreen_run.hpp
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include/ncbi-tools++/algo/blast/igblast/igblast.hpp
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include/ncbi-tools++/algo/dustmask/sdust.tex
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include/ncbi-tools++/algo/dustmask/symdust.hpp
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include/ncbi-tools++/algo/segmask/segmask.hpp
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include/ncbi-tools++/algo/winmask/README.API
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include/ncbi-tools++/algo/winmask/seq_masker.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_cache_boost.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_istat.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_istat_ascii.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_istat_bin.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_istat_factory.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_istat_oascii.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_istat_obinary.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_ostat.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_ostat_ascii.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_ostat_bin.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_ostat_factory.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_ostat_opt.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_ostat_opt_ascii.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_ostat_opt_bin.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_score.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_score_mean.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_score_mean_glob.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_score_min.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_uset_array.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_uset_hash.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_uset_simple.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_util.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_window.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_window_ambig.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_window_pattern.hpp
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include/ncbi-tools++/algo/winmask/seq_masker_window_pattern_ambig.hpp
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include/ncbi-tools++/algo/winmask/win_mask_config.hpp
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include/ncbi-tools++/algo/winmask/win_mask_counts_converter.hpp
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include/ncbi-tools++/algo/winmask/win_mask_dup_table.hpp
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include/ncbi-tools++/algo/winmask/win_mask_gen_counts.hpp
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include/ncbi-tools++/algo/winmask/win_mask_util.hpp
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include/ncbi-tools++/cgi/caf.hpp
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include/ncbi-tools++/cgi/caf_encoded.hpp
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include/ncbi-tools++/cgi/caf_plain.hpp
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include/ncbi-tools++/cgi/cgi_exception.hpp
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include/ncbi-tools++/cgi/cgi_serial.hpp
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include/ncbi-tools++/cgi/cgi_session.hpp
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include/ncbi-tools++/cgi/cgi_util.hpp
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include/ncbi-tools++/cgi/cgiapp.hpp
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include/ncbi-tools++/cgi/cgiapp_cached.hpp
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include/ncbi-tools++/cgi/cgictx.hpp
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include/ncbi-tools++/cgi/error_codes.hpp
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include/ncbi-tools++/cgi/impl/cgi_entry_reader.hpp
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include/ncbi-tools++/cgi/ncbicgi.hpp
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include/ncbi-tools++/cgi/ncbicgir.hpp
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include/ncbi-tools++/cgi/ncbires.hpp
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include/ncbi-tools++/cgi/ref_args.hpp
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include/ncbi-tools++/cgi/user_agent.hpp
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include/ncbi-tools++/common/config/ncbiconf_msvc.h
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include/ncbi-tools++/common/config/ncbiconf_msvc_site.h
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include/ncbi-tools++/common/config/ncbiconf_universal.h
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include/ncbi-tools++/common/config/ncbiconf_xcode.h
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include/ncbi-tools++/common/config/ncbiconf_xcode_site.h
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include/ncbi-tools++/common/header_template.hpp
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include/ncbi-tools++/common/metamodules_doxygen.h
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include/ncbi-tools++/common/ncbi_export.h
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include/ncbi-tools++/common/ncbi_package_ver.h
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include/ncbi-tools++/common/ncbi_pch_impl.hpp
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include/ncbi-tools++/common/ncbi_skew_guard.h
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include/ncbi-tools++/common/ncbi_source_ver.h
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include/ncbi-tools++/common/ncbiconf_impl.h
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include/ncbi-tools++/common/test_assert.h
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include/ncbi-tools++/common/test_assert_impl.h
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include/ncbi-tools++/common/test_data_path.h
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include/ncbi-tools++/connect/connect_export.h
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include/ncbi-tools++/connect/email_diag_handler.hpp
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include/ncbi-tools++/connect/error_codes.hpp
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include/ncbi-tools++/connect/ext/ncbi_crypt.h
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include/ncbi-tools++/connect/ext/ncbi_dblb.h
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include/ncbi-tools++/connect/ext/ncbi_dblb_svcmapper.hpp
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include/ncbi-tools++/connect/ext/ncbi_ifconf.h
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include/ncbi-tools++/connect/ext/ncbi_iprange.h
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include/ncbi-tools++/connect/ext/ncbi_localnet.h
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include/ncbi-tools++/connect/impl/server_connection.hpp
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include/ncbi-tools++/connect/impl/thread_pool_for_server.hpp
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include/ncbi-tools++/connect/ncbi_base64.h
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include/ncbi-tools++/connect/ncbi_buffer.h
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include/ncbi-tools++/connect/ncbi_conn_exception.hpp
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include/ncbi-tools++/connect/ncbi_conn_reader_writer.hpp
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include/ncbi-tools++/connect/ncbi_conn_stream.hpp
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include/ncbi-tools++/connect/ncbi_conn_test.hpp
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include/ncbi-tools++/connect/ncbi_connection.h
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include/ncbi-tools++/connect/ncbi_connector.h
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include/ncbi-tools++/connect/ncbi_connutil.h
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include/ncbi-tools++/connect/ncbi_core.h
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include/ncbi-tools++/connect/ncbi_core_cxx.hpp
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include/ncbi-tools++/connect/ncbi_file_connector.h
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include/ncbi-tools++/connect/ncbi_ftp_connector.h
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include/ncbi-tools++/connect/ncbi_gnutls.h
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include/ncbi-tools++/connect/ncbi_heapmgr.h
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include/ncbi-tools++/connect/ncbi_host_info.h
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include/ncbi-tools++/connect/ncbi_http_connector.h
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include/ncbi-tools++/connect/ncbi_http_session.hpp
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include/ncbi-tools++/connect/ncbi_memory_connector.h
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include/ncbi-tools++/connect/ncbi_misc.hpp
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include/ncbi-tools++/connect/ncbi_namedpipe.hpp
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include/ncbi-tools++/connect/ncbi_namedpipe_connector.hpp
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include/ncbi-tools++/connect/ncbi_pipe.hpp
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include/ncbi-tools++/connect/ncbi_pipe_connector.hpp
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include/ncbi-tools++/connect/ncbi_sendmail.h
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include/ncbi-tools++/connect/ncbi_server_info.h
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include/ncbi-tools++/connect/ncbi_service.h
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include/ncbi-tools++/connect/ncbi_service_connector.h
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include/ncbi-tools++/connect/ncbi_socket.h
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include/ncbi-tools++/connect/ncbi_socket.hpp
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include/ncbi-tools++/connect/ncbi_socket_connector.h
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include/ncbi-tools++/connect/ncbi_socket_unix.h
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include/ncbi-tools++/connect/ncbi_socket_unix.hpp
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include/ncbi-tools++/connect/ncbi_types.h
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include/ncbi-tools++/connect/ncbi_userhost.hpp
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include/ncbi-tools++/connect/ncbi_util.h
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include/ncbi-tools++/connect/server.hpp
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include/ncbi-tools++/connect/server_monitor.hpp
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include/ncbi-tools++/connect/services/blob_storage_netcache.hpp
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include/ncbi-tools++/connect/services/clparser.hpp
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include/ncbi-tools++/connect/services/compound_id.hpp
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include/ncbi-tools++/connect/services/error_codes.hpp
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include/ncbi-tools++/connect/services/grid_app_version_info.hpp
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include/ncbi-tools++/connect/services/grid_client.hpp
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include/ncbi-tools++/connect/services/grid_client_app.hpp
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include/ncbi-tools++/connect/services/grid_control_thread.hpp
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include/ncbi-tools++/connect/services/grid_globals.hpp
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include/ncbi-tools++/objects/homologene/HG_Commentary.hpp
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include/ncbi-tools++/objects/homologene/HG_CommentaryContainer.hpp
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include/ncbi-tools++/objects/homologene/HG_Entry_.hpp
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include/ncbi-tools++/objects/homologene/HG_Gene.hpp
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include/ncbi-tools++/objects/homologene/HG_Gene_.hpp
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include/ncbi-tools++/objects/homologene/HG_Link.hpp
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include/ncbi-tools++/objects/homologene/HG_Node.hpp
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include/ncbi-tools++/objects/homologene/HomoloGene_module.hpp
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