biology/seqan: update 1.3.1 -> 2.1.1

biology/seqan1: create port from current SeqAn 1.3.1 for legacy usage
UPDATING: document SeqAn updates and seqan1 port for legacy usage

PR:		204127
Submitted by:	Hannes Hauswedell <h2+fbsdports@fsfe.org>

12 files changed, 3706 insertions, 1915 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 4a21bff385f4..68aaba32ad79 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -91,6 +91,7 @@
     SUBDIR += seaview
     SUBDIR += seqan
     SUBDIR += seqan-apps
+    SUBDIR += seqan1
     SUBDIR += seqio
     SUBDIR += seqtools
     SUBDIR += sim4
diff --git a/biology/seqan/Makefile b/biology/seqan/Makefile
index 2abf70d857b0..60663f571dd3 100644
--- a/biology/seqan/Makefile
+++ b/biology/seqan/Makefile
@@ -2,33 +2,31 @@
 # $FreeBSD$
 
 PORTNAME=	seqan
-PORTVERSION=	1.3.1
-PORTREVISION=	3
+PORTVERSION=	2.1.1
 CATEGORIES=	biology
-MASTER_SITES=	http://ftp.seqan.de/releases/
+MASTER_SITES=	http://packages.seqan.de/seqan-library/
+DISTNAME=	${PORTNAME}-library-${PORTVERSION}
 
 MAINTAINER=	h2+fbsdports@fsfe.org
-COMMENT=	C++ Sequence Analysis Library
+COMMENT=	C++ Sequence Analysis Template Library
 
-LICENSE=	BSD3CLAUSE GPLv3
-LICENSE_COMB=	multi
+LICENSE=	BSD3CLAUSE
+LICENSE_FILE=	${WRKSRC}/share/doc/seqan/LICENSE
 
-LICENSE_FILE_BSD=${WRKSRC}/seqan/LICENSE
-LICENSE_FILE_GPLv3=${WRKSRC}/apps/LICENSE
+USES=		tar:xz
+NO_BUILD=	yes
 
-USES=		cmake:outsource python:build zip
-CMAKE_SOURCE_PATH=${WRKSRC}/cmake
-MAKE_JOB_SAFE=	yes
+CONFLICTS=	seqan1-[0-9]*
 
-SUB_FILES=	pkg-message
-PKG_MESSAGE=	${WRKDIR}/pkg-message
+OPTIONS_DEFINE=	DOCS
+DOCS_DESC=	Install official API documentation (html)
 
-USE_GCC=	4.8
+do-install:
+	${MKDIR} ${STAGEDIR}/${PREFIX}/include/${PORTNAME}
+	cd ${WRKSRC}/include/ && ${COPYTREE_SHARE} ./${PORTNAME} ${STAGEDIR}/${PREFIX}/include
 
-# unsafe workaround because FreeBSD lacks logl and expl
-# see "BUGS" in `man 3 math`
-post-patch:
-	@${REINPLACE_CMD} -e 's|expl|exp|g' ${WRKSRC}/apps/snp_store/snp_store.h
-	@${REINPLACE_CMD} -e 's|logl|log|g' ${WRKSRC}/apps/snp_store/snp_store.h
+post-install:
+	${MKDIR} ${STAGEDIR}${DOCSDIR}
+	cd ${WRKSRC}/share/doc/ && ${COPYTREE_SHARE} ./seqan/ ${STAGEDIR}${DOCSDIR}/../
 
 .include <bsd.port.mk>
diff --git a/biology/seqan/distinfo b/biology/seqan/distinfo
index 3e7a0a49d7b4..ab08fbcf3252 100644
--- a/biology/seqan/distinfo
+++ b/biology/seqan/distinfo
@@ -1,2 +1,2 @@
-SHA256 (seqan-1.3.1.zip) = 87eebe73ace9ada2f4664a768ae212d4acc5fb3ce87702709c3d15bf2d153aeb
-SIZE (seqan-1.3.1.zip) = 8787521
+SHA256 (seqan-library-2.1.1.tar.xz) = 8926f91fec5ce57e8efc70ac16cbf041bde0e0be463685b86e0d2e1e6a8169d7
+SIZE (seqan-library-2.1.1.tar.xz) = 5238884
diff --git a/biology/seqan/files/patch-cmake-CMakeLists.txt b/biology/seqan/files/patch-cmake-CMakeLists.txt
deleted file mode 100644
index 8f39eebd62f6..000000000000
--- a/biology/seqan/files/patch-cmake-CMakeLists.txt
+++ /dev/null
@@ -1,13 +0,0 @@
---- cmake/CMakeLists.txt.orig	2012-05-04 12:56:23.000000000 +0800
-+++ cmake/CMakeLists.txt	2012-05-04 13:00:03.000000000 +0800
-@@ -146,6 +146,10 @@
-             COMPONENT headers)
-     #message("install(FILES ${HEADER} RENAME seqan${NEW_PATH} DESTINATION include COMPONENT headers)")
- endforeach()
-+#seqan.h
-+install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../seqan.h
-+	DESTINATION include
-+	COMPONENT headers)
- 
- ################################################################################
- # Set Compiler Flags
diff --git a/biology/seqan/files/patch-cmake-apps-CMakeLists.txt b/biology/seqan/files/patch-cmake-apps-CMakeLists.txt
deleted file mode 100644
index 21f5acf7b97f..000000000000
--- a/biology/seqan/files/patch-cmake-apps-CMakeLists.txt
+++ /dev/null
@@ -1,8 +0,0 @@
---- cmake/apps/CMakeLists.txt.orig	2012-05-04 11:12:35.000000000 +0800
-+++ cmake/apps/CMakeLists.txt	2012-05-04 11:23:26.000000000 +0800
-@@ -108,4 +108,4 @@
- 
- # Install RazerS gapped parameters.
- install(DIRECTORY ${SEQAN_LIBRARY}/apps/razers2/gapped_params
--        DESTINATION bin)
-+        DESTINATION share/seqan)
diff --git a/biology/seqan/files/pkg-message.in b/biology/seqan/files/pkg-message.in
deleted file mode 100644
index 71fbb10d6371..000000000000
--- a/biology/seqan/files/pkg-message.in
+++ /dev/null
@@ -1,6 +0,0 @@
-gapped_params for Razers2 have been installed to 
-      %%PREFIX%%/share/seqan/gapped_params
-      
-If you require these, make sure to set the correct 
-path with --param-dir as Razers2 will not pick them 
-up automatically.
diff --git a/biology/seqan/pkg-descr b/biology/seqan/pkg-descr
index 298ab519446f..705046885848 100644
--- a/biology/seqan/pkg-descr
+++ b/biology/seqan/pkg-descr
@@ -3,4 +3,7 @@ and data structures for the analysis of sequences with the
 focus on biological data. The library is licensed under the
 3-clause BSD license except the applications which are GPL.
 
+This port now only contains the header library and API
+documentation. The apps are separate.
+
 WWW: http://www.seqan.de/
diff --git a/biology/seqan/pkg-plist b/biology/seqan/pkg-plist
index 4e5828318deb..4592c53d4e0c 100644
--- a/biology/seqan/pkg-plist
+++ b/biology/seqan/pkg-plist
@@ -1,169 +1,227 @@
-bin/dfi
-bin/insegt
-bin/mason
-bin/micro_razers
-bin/pair_align
-bin/param_chooser
-bin/rabema
-bin/razers
-bin/razers2
-bin/rep_sep
-bin/sak
-bin/seqan_tcoffee
-bin/seqcons
-bin/snp_store
-bin/splazers
-bin/stellar
-bin/tree_recon
-include/seqan.h
 include/seqan/align.h
-include/seqan/align/align_algorithms.h
 include/seqan/align/align_base.h
-include/seqan/align/align_cols_base.h
-include/seqan/align/align_dynprog.h
-include/seqan/align/align_generated_forwards.h
-include/seqan/align/align_hirschberg.h
+include/seqan/align/align_cols.h
+include/seqan/align/align_config.h
 include/seqan/align/align_iterator_base.h
-include/seqan/align/align_local_dynprog.h
-include/seqan/align/align_local_dynprog_banded.h
-include/seqan/align/align_myers.h
-include/seqan/align/align_trace.h
+include/seqan/align/align_metafunctions.h
+include/seqan/align/align_traceback.h
+include/seqan/align/alignment_algorithm_tags.h
+include/seqan/align/alignment_operations.h
+include/seqan/align/dp_algorithm_impl.h
+include/seqan/align/dp_band.h
+include/seqan/align/dp_cell.h
+include/seqan/align/dp_cell_affine.h
+include/seqan/align/dp_cell_dynamic.h
+include/seqan/align/dp_cell_linear.h
+include/seqan/align/dp_context.h
+include/seqan/align/dp_formula.h
+include/seqan/align/dp_formula_affine.h
+include/seqan/align/dp_formula_dynamic.h
+include/seqan/align/dp_formula_linear.h
+include/seqan/align/dp_matrix.h
+include/seqan/align/dp_matrix_navigator.h
+include/seqan/align/dp_matrix_navigator_score_matrix.h
+include/seqan/align/dp_matrix_navigator_score_matrix_sparse.h
+include/seqan/align/dp_matrix_navigator_trace_matrix.h
+include/seqan/align/dp_matrix_sparse.h
+include/seqan/align/dp_meta_info.h
+include/seqan/align/dp_profile.h
+include/seqan/align/dp_scout.h
+include/seqan/align/dp_setup.h
+include/seqan/align/dp_trace_segment.h
+include/seqan/align/dp_traceback_adaptor.h
+include/seqan/align/dp_traceback_impl.h
+include/seqan/align/evaluate_alignment.h
+include/seqan/align/fragment.h
+include/seqan/align/gap_anchor.h
+include/seqan/align/gapped_value_type.h
+include/seqan/align/gaps_anchor.h
 include/seqan/align/gaps_array.h
 include/seqan/align/gaps_base.h
+include/seqan/align/gaps_iterator_anchor.h
+include/seqan/align/gaps_iterator_array.h
 include/seqan/align/gaps_iterator_base.h
-include/seqan/align/gaps_sumlist.h
-include/seqan/align/hirschberg_set.h
+include/seqan/align/global_alignment_banded.h
+include/seqan/align/global_alignment_hirschberg_impl.h
+include/seqan/align/global_alignment_myers_hirschberg_impl.h
+include/seqan/align/global_alignment_myers_impl.h
+include/seqan/align/global_alignment_specialized.h
+include/seqan/align/global_alignment_unbanded.h
+include/seqan/align/local_alignment_banded.h
+include/seqan/align/local_alignment_banded_waterman_eggert_impl.h
+include/seqan/align/local_alignment_enumeration.h
+include/seqan/align/local_alignment_enumeration_banded.h
+include/seqan/align/local_alignment_enumeration_unbanded.h
+include/seqan/align/local_alignment_unbanded.h
+include/seqan/align/local_alignment_waterman_eggert_impl.h
 include/seqan/align/matrix_base.h
+include/seqan/align_extend.h
+include/seqan/align_extend/align_extend.h
+include/seqan/align_extend/align_extend_base.h
+include/seqan/align_extend/dp_scout_xdrop.h
+include/seqan/align_profile.h
+include/seqan/align_profile/add_to_profile.h
+include/seqan/align_profile/score_profile_seq.h
+include/seqan/align_split.h
+include/seqan/align_split/align_split_interface.h
+include/seqan/align_split/dp_scout_split.h
+include/seqan/alignment_free.h
+include/seqan/alignment_free/af_d2.h
+include/seqan/alignment_free/af_d2star.h
+include/seqan/alignment_free/af_d2z.h
+include/seqan/alignment_free/af_n2.h
+include/seqan/alignment_free/alignment_free_base.h
+include/seqan/alignment_free/alignment_free_comparison.h
+include/seqan/alignment_free/kmer_functions.h
+include/seqan/arg_parse.h
+include/seqan/arg_parse/arg_parse_argument.h
+include/seqan/arg_parse/arg_parse_ctd_support.h
+include/seqan/arg_parse/arg_parse_doc.h
+include/seqan/arg_parse/arg_parse_exceptions.h
+include/seqan/arg_parse/arg_parse_option.h
+include/seqan/arg_parse/arg_parse_parse.h
+include/seqan/arg_parse/arg_parse_type_support.h
+include/seqan/arg_parse/argument_parser.h
+include/seqan/arg_parse/tool_doc.h
+include/seqan/arg_parse/xml_support.h
+include/seqan/bam_io.h
+include/seqan/bam_io/bam_alignment_record.h
+include/seqan/bam_io/bam_alignment_record_util.h
+include/seqan/bam_io/bam_file.h
+include/seqan/bam_io/bam_header_record.h
+include/seqan/bam_io/bam_index_bai.h
+include/seqan/bam_io/bam_io_context.h
+include/seqan/bam_io/bam_sam_conversion.h
+include/seqan/bam_io/bam_scanner_cache.h
+include/seqan/bam_io/bam_tags_dict.h
+include/seqan/bam_io/cigar.h
+include/seqan/bam_io/read_bam.h
+include/seqan/bam_io/read_sam.h
+include/seqan/bam_io/write_bam.h
+include/seqan/bam_io/write_sam.h
 include/seqan/basic.h
-include/seqan/basic/basic_aggregates.h
-include/seqan/basic/basic_allocator_chunkpool.h
-include/seqan/basic/basic_allocator_interface.h
-include/seqan/basic/basic_allocator_multipool.h
-include/seqan/basic/basic_allocator_simple.h
-include/seqan/basic/basic_allocator_singlepool.h
-include/seqan/basic/basic_allocator_to_std.h
-include/seqan/basic/basic_alphabet_interface.h
-include/seqan/basic/basic_alphabet_interface2.h
-include/seqan/basic/basic_alphabet_simple.h
-include/seqan/basic/basic_alphabet_simple_tabs.h
-include/seqan/basic/basic_alphabet_trait_basic.h
-include/seqan/basic/basic_compare.h
-include/seqan/basic/basic_converter.h
-include/seqan/basic/basic_counted_ptr.h
+include/seqan/basic/aggregate_concept.h
+include/seqan/basic/allocator_chunkpool.h
+include/seqan/basic/allocator_interface.h
+include/seqan/basic/allocator_multipool.h
+include/seqan/basic/allocator_simple.h
+include/seqan/basic/allocator_singlepool.h
+include/seqan/basic/allocator_to_std.h
+include/seqan/basic/alphabet_adapt_builtins.h
+include/seqan/basic/alphabet_bio.h
+include/seqan/basic/alphabet_concept.h
+include/seqan/basic/alphabet_math.h
+include/seqan/basic/alphabet_profile.h
+include/seqan/basic/alphabet_qualities.h
+include/seqan/basic/alphabet_residue.h
+include/seqan/basic/alphabet_residue_funcs.h
+include/seqan/basic/alphabet_residue_tabs.h
+include/seqan/basic/alphabet_simple_type.h
+include/seqan/basic/alphabet_storage.h
+include/seqan/basic/array_construct_destruct.h
+include/seqan/basic/basic_aggregate.h
+include/seqan/basic/basic_allocator.h
+include/seqan/basic/basic_alphabet.h
+include/seqan/basic/basic_concept.h
+include/seqan/basic/basic_container.h
 include/seqan/basic/basic_debug.h
-include/seqan/basic/basic_definition.h
-include/seqan/basic/basic_forwards.h
-include/seqan/basic/basic_generated_forwards.h
-include/seqan/basic/basic_holder.h
-include/seqan/basic/basic_holder_dynamic.h
-include/seqan/basic/basic_host.h
+include/seqan/basic/basic_device.h
+include/seqan/basic/basic_exception.h
+include/seqan/basic/basic_functors.h
+include/seqan/basic/basic_fundamental.h
 include/seqan/basic/basic_iterator.h
-include/seqan/basic/basic_iterator_adapt_std.h
-include/seqan/basic/basic_iterator_adaptor.h
-include/seqan/basic/basic_iterator_base.h
-include/seqan/basic/basic_iterator_position.h
-include/seqan/basic/basic_iterator_simple.h
-include/seqan/basic/basic_logvalue.h
+include/seqan/basic/basic_math.h
 include/seqan/basic/basic_metaprogramming.h
-include/seqan/basic/basic_operator.h
 include/seqan/basic/basic_parallelism.h
-include/seqan/basic/basic_pointer.h
-include/seqan/basic/basic_profchar.h
-include/seqan/basic/basic_profile.h
 include/seqan/basic/basic_proxy.h
-include/seqan/basic/basic_sse2.h
-include/seqan/basic/basic_tag.h
-include/seqan/basic/basic_testing.h
-include/seqan/basic/basic_transport.h
+include/seqan/basic/basic_simd_vector.h
+include/seqan/basic/basic_smart_pointer.h
+include/seqan/basic/basic_stream.h
+include/seqan/basic/basic_tangle.h
 include/seqan/basic/basic_type.h
-include/seqan/basic/basic_volatile_ptr.h
+include/seqan/basic/basic_view.h
+include/seqan/basic/boost_preprocessor_subset.h
+include/seqan/basic/builtin_functions.h
+include/seqan/basic/concept_checking.h
+include/seqan/basic/container_concept.h
+include/seqan/basic/debug_helper.h
+include/seqan/basic/debug_test_system.h
+include/seqan/basic/fundamental_chunking.h
+include/seqan/basic/fundamental_comparison.h
+include/seqan/basic/fundamental_concepts.h
+include/seqan/basic/fundamental_conversion.h
+include/seqan/basic/fundamental_metafunctions.h
+include/seqan/basic/fundamental_tags.h
+include/seqan/basic/fundamental_transport.h
+include/seqan/basic/holder_base.h
+include/seqan/basic/holder_simple.h
+include/seqan/basic/holder_tristate.h
+include/seqan/basic/hosted_type_interface.h
+include/seqan/basic/iterator_adapt_pointer.h
+include/seqan/basic/iterator_adapt_std.h
+include/seqan/basic/iterator_adaptor.h
+include/seqan/basic/iterator_base.h
+include/seqan/basic/iterator_concept.h
+include/seqan/basic/iterator_counting.h
+include/seqan/basic/iterator_interface.h
+include/seqan/basic/iterator_position.h
+include/seqan/basic/iterator_range.h
+include/seqan/basic/iterator_zip.h
+include/seqan/basic/macro_deprecated.h
+include/seqan/basic/math_functions.h
+include/seqan/basic/math_log_space_value.h
+include/seqan/basic/metaprogramming_control.h
+include/seqan/basic/metaprogramming_enable_if.h
+include/seqan/basic/metaprogramming_logic.h
+include/seqan/basic/metaprogramming_math.h
+include/seqan/basic/metaprogramming_type.h
+include/seqan/basic/metaprogramming_type_algebra.h
+include/seqan/basic/pair_base.h
+include/seqan/basic/pair_bit_compressed.h
+include/seqan/basic/pair_packed.h
+include/seqan/basic/profiling.h
+include/seqan/basic/property_map_concept.h
+include/seqan/basic/proxy_base.h
+include/seqan/basic/proxy_iterator.h
+include/seqan/basic/test_system.h
+include/seqan/basic/triple_base.h
+include/seqan/basic/triple_packed.h
+include/seqan/basic/tuple_base.h
+include/seqan/basic/tuple_bit_compressed.h
+include/seqan/basic/volatile_ptr.h
+include/seqan/bed_io.h
+include/seqan/bed_io/bed_file.h
+include/seqan/bed_io/bed_record.h
+include/seqan/bed_io/read_bed.h
+include/seqan/bed_io/write_bed.h
 include/seqan/blast.h
 include/seqan/blast/blast_base.h
-include/seqan/blast/blast_generated_forwards.h
-include/seqan/blast/blast_hit.h
-include/seqan/blast/blast_hit_iterator.h
-include/seqan/blast/blast_hsp.h
-include/seqan/blast/blast_hsp_iterator.h
-include/seqan/blast/blast_iterator.h
-include/seqan/blast/blast_parsing.h
-include/seqan/blast/blast_report.h
-include/seqan/blast/blast_run.h
-include/seqan/blast/blast_stream_hit.h
-include/seqan/blast/blast_stream_hit_iterator.h
-include/seqan/blast/blast_stream_hsp_iterator.h
-include/seqan/blast/blast_stream_report.h
-include/seqan/chaining.h
-include/seqan/chaining/chain_base.h
-include/seqan/chaining/chain_generic.h
-include/seqan/chaining/chain_meta_fragment.h
-include/seqan/chaining/chain_point.h
-include/seqan/chaining/chain_wrapper_point.h
-include/seqan/chaining/chaining_generated_forwards.h
-include/seqan/chaining/fragment.h
-include/seqan/chaining/geom_distribution.h
-include/seqan/chaining/range_max_tree.h
-include/seqan/chaining/range_tree.h
-include/seqan/chaining/rmt_base.h
-include/seqan/chaining/rmt_common_algos.h
-include/seqan/chaining/rmt_compl_algos.h
-include/seqan/chaining/rmt_def_algos.h
-include/seqan/chaining/rmt_skip_base_element.h
-include/seqan/chaining/rmt_skip_element.h
-include/seqan/chaining/rt_base.h
-include/seqan/chaining/rt_common_algos.h
-include/seqan/chaining/rt_impl.h
-include/seqan/chaining/rt_skip_base_element.h
-include/seqan/chaining/rt_skip_element.h
-include/seqan/chaining/rt_sl_base.h
-include/seqan/chaining/rt_sl_compl_algos.h
-include/seqan/chaining/rt_sl_def_algos.h
-include/seqan/chaining/rt_sl_impl.h
-include/seqan/chaining/score_chain.h
-include/seqan/chaining/score_chain_sop.h
-include/seqan/chaining/score_manhattan.h
-include/seqan/chaining/score_zero.h
-include/seqan/chaining/skip_base_element.h
-include/seqan/chaining/skip_element.h
-include/seqan/chaining/skip_list.h
-include/seqan/chaining/skip_list_base.h
-include/seqan/chaining/skip_list_dynamic.h
-include/seqan/chaining/skip_list_impl.h
-include/seqan/chaining/skip_list_iterator.h
-include/seqan/chaining/skip_list_type.h
-include/seqan/chaining/skip_pool_alloc.h
-include/seqan/chaining/tree_chain.h
-include/seqan/chaining/tree_chain_sop.h
-include/seqan/chaining/tree_chain_utils.h
+include/seqan/blast/blast_io_context.h
+include/seqan/blast/blast_record.h
+include/seqan/blast/blast_report_out.h
+include/seqan/blast/blast_statistics.h
+include/seqan/blast/blast_tabular.h
+include/seqan/blast/blast_tabular_in.h
+include/seqan/blast/blast_tabular_lowlevel.h
+include/seqan/blast/blast_tabular_out.h
 include/seqan/consensus.h
+include/seqan/consensus/consensus_aligner.h
+include/seqan/consensus/consensus_aligner_interface.h
+include/seqan/consensus/consensus_alignment_options.h
 include/seqan/consensus/consensus_base.h
-include/seqan/consensus/consensus_generated_forwards.h
+include/seqan/consensus/consensus_builder.h
 include/seqan/consensus/consensus_library.h
 include/seqan/consensus/consensus_realign.h
 include/seqan/consensus/consensus_score.h
+include/seqan/consensus/overlap_info_computation.h
+include/seqan/consensus/overlapper.h
 include/seqan/file.h
-include/seqan/file/chunk_collector.h
-include/seqan/file/cstream.h
-include/seqan/file/file_array.h
 include/seqan/file/file_base.h
 include/seqan/file/file_cstyle.h
-include/seqan/file/file_filereader.h
-include/seqan/file/file_filereaderiterator.h
-include/seqan/file/file_format.h
-include/seqan/file/file_format_cgviz.h
-include/seqan/file/file_format_embl.h
-include/seqan/file/file_format_fasta.h
-include/seqan/file/file_format_fasta_align.h
-include/seqan/file/file_format_genbank.h
-include/seqan/file/file_format_guess.h
-include/seqan/file/file_format_mmap.h
-include/seqan/file/file_format_raw.h
 include/seqan/file/file_forwards.h
-include/seqan/file/file_generated_forwards.h
+include/seqan/file/file_interface.h
+include/seqan/file/file_mapping.h
 include/seqan/file/file_page.h
-include/seqan/file/file_page_raid0.h
-include/seqan/file/meta.h
-include/seqan/file/stream.h
-include/seqan/file/stream_algorithms.h
 include/seqan/file/string_external.h
 include/seqan/file/string_mmap.h
 include/seqan/find.h
@@ -173,9 +231,9 @@ include/seqan/find/find_base.h
 include/seqan/find/find_begin.h
 include/seqan/find/find_bndm.h
 include/seqan/find/find_bom.h
-include/seqan/find/find_generated_forwards.h
 include/seqan/find/find_hamming_simple.h
 include/seqan/find/find_horspool.h
+include/seqan/find/find_lambda.h
 include/seqan/find/find_multi.h
 include/seqan/find/find_multiple_bfam.h
 include/seqan/find/find_multiple_shiftand.h
@@ -189,50 +247,42 @@ include/seqan/find/find_shiftor.h
 include/seqan/find/find_simple.h
 include/seqan/find/find_wild_shiftand.h
 include/seqan/find/find_wumanber.h
-include/seqan/find2.h
-include/seqan/find2/find2_generated_forwards.h
-include/seqan/find2/find_approx_dpsearch.h
-include/seqan/find2/find_approx_find_begin.h
-include/seqan/find2/find_base.h
-include/seqan/find2/find_exact_shiftand.h
-include/seqan/find2/find_exact_simple.h
-include/seqan/find2/find_finder_default.h
-include/seqan/find2/find_hamming_simple.h
-include/seqan/find2/find_multiple_exact_simple.h
-include/seqan/find2/find_pattern_wild_shiftand.h
-include/seqan/find_motif.h
-include/seqan/find_motif/em_algorithm.h
-include/seqan/find_motif/find_motif_base.h
-include/seqan/find_motif/find_motif_epatternbranching.h
-include/seqan/find_motif/find_motif_generated_forwards.h
-include/seqan/find_motif/find_motif_pms1.h
-include/seqan/find_motif/find_motif_pmsp.h
-include/seqan/find_motif/find_motif_projection.h
-include/seqan/find_motif/frequency_distribution.h
-include/seqan/find_motif/profile.h
-include/seqan/find_motif/pseudocount_base.h
-include/seqan/find_motif/pseudocount_mode_c.h
-include/seqan/find_motif/pseudocount_mode_p.h
-include/seqan/find_motif/sequence_model_types.h
+include/seqan/gff_io.h
+include/seqan/gff_io/gff_file.h
+include/seqan/gff_io/gff_io_base.h
 include/seqan/graph_algorithms.h
-include/seqan/graph_algorithms/graph_algorithm.h
+include/seqan/graph_algorithms/all_pairs_shortest_path.h
+include/seqan/graph_algorithms/bellman_ford.h
+include/seqan/graph_algorithms/bipartite_matching.h
+include/seqan/graph_algorithms/breadth_first_search.h
+include/seqan/graph_algorithms/connected_components.h
+include/seqan/graph_algorithms/depth_first_search.h
+include/seqan/graph_algorithms/dijkstra.h
+include/seqan/graph_algorithms/floyd_warshall.h
+include/seqan/graph_algorithms/ford_fulkerson.h
 include/seqan/graph_algorithms/graph_algorithm_heap_tree.h
 include/seqan/graph_algorithms/graph_algorithm_hmm.h
 include/seqan/graph_algorithms/graph_algorithm_lis_his.h
-include/seqan/graph_algorithms/graph_algorithms_generated_forwards.h
+include/seqan/graph_algorithms/kruskal.h
+include/seqan/graph_algorithms/path_growing.h
+include/seqan/graph_algorithms/prim.h
+include/seqan/graph_algorithms/single_source_shortest_path.h
+include/seqan/graph_algorithms/strongly_connected_compnents.h
+include/seqan/graph_algorithms/topological_sort.h
+include/seqan/graph_algorithms/transitive_closure.h
+include/seqan/graph_algorithms/weakly_connected_components.h
+include/seqan/graph_algorithms/weighted_bipartite_matching.h
 include/seqan/graph_align.h
-include/seqan/graph_align/graph_align_banded_gotoh.h
-include/seqan/graph_align/graph_align_banded_needleman_wunsch.h
-include/seqan/graph_align/graph_align_banded_smith_waterman_clump.h
-include/seqan/graph_align/graph_align_base.h
-include/seqan/graph_align/graph_align_config.h
-include/seqan/graph_align/graph_align_generated_forwards.h
-include/seqan/graph_align/graph_align_gotoh.h
-include/seqan/graph_align/graph_align_hirschberg.h
-include/seqan/graph_align/graph_align_interface.h
-include/seqan/graph_align/graph_align_needleman_wunsch.h
-include/seqan/graph_align/graph_align_smith_waterman.h
-include/seqan/graph_align/graph_align_smith_waterman_clump.h
+include/seqan/graph_align/graph_algorithm_refine_align.h
+include/seqan/graph_align/graph_algorithm_refine_aligngraph.h
+include/seqan/graph_align/graph_algorithm_refine_annotation.h
+include/seqan/graph_align/graph_algorithm_refine_exact.h
+include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h
+include/seqan/graph_align/graph_algorithm_refine_fragment.h
+include/seqan/graph_align/graph_algorithm_refine_inexact.h
+include/seqan/graph_align/graph_algorithm_refine_scoring.h
+include/seqan/graph_align/graph_impl_align.h
+include/seqan/graph_align/graph_impl_align_adapt.h
 include/seqan/graph_msa.h
 include/seqan/graph_msa/graph_align_tcoffee_base.h
 include/seqan/graph_msa/graph_align_tcoffee_distance.h
@@ -243,7 +293,6 @@ include/seqan/graph_msa/graph_align_tcoffee_library.h
 include/seqan/graph_msa/graph_align_tcoffee_msa.h
 include/seqan/graph_msa/graph_align_tcoffee_progressive.h
 include/seqan/graph_msa/graph_align_tcoffee_refinement.h
-include/seqan/graph_msa/graph_msa_generated_forwards.h
 include/seqan/graph_types.h
 include/seqan/graph_types/graph_base.h
 include/seqan/graph_types/graph_drawing.h
@@ -251,7 +300,6 @@ include/seqan/graph_types/graph_edgestump.h
 include/seqan/graph_types/graph_idmanager.h
 include/seqan/graph_types/graph_impl_automaton.h
 include/seqan/graph_types/graph_impl_directed.h
-include/seqan/graph_types/graph_impl_fragment.h
 include/seqan/graph_types/graph_impl_hmm.h
 include/seqan/graph_types/graph_impl_oracle.h
 include/seqan/graph_types/graph_impl_tree.h
@@ -266,44 +314,74 @@ include/seqan/graph_types/graph_iterator_dfs.h
 include/seqan/graph_types/graph_iterator_edge.h
 include/seqan/graph_types/graph_iterator_outedge.h
 include/seqan/graph_types/graph_iterator_vertex.h
-include/seqan/graph_types/graph_property.h
-include/seqan/graph_types/graph_types_generated_forwards.h
 include/seqan/graph_types/graph_utility_parsing.h
+include/seqan/graph_types/property_map_generic.h
+include/seqan/graph_types/property_map_internal.h
+include/seqan/graph_types/property_map_internal_pointer.h
 include/seqan/index.h
+include/seqan/index/find2_backtracking.h
+include/seqan/index/find2_base.h
+include/seqan/index/find2_functors.h
+include/seqan/index/find2_index.h
+include/seqan/index/find2_index_multi.h
+include/seqan/index/find2_vstree_factory.h
+include/seqan/index/find_backtracking.h
 include/seqan/index/find_index.h
 include/seqan/index/find_index_approx.h
+include/seqan/index/find_index_binary.h
 include/seqan/index/find_index_esa.h
+include/seqan/index/find_index_lambda.h
 include/seqan/index/find_index_qgram.h
+include/seqan/index/find_pigeonhole.h
 include/seqan/index/find_quasar.h
 include/seqan/index/find_swift.h
 include/seqan/index/index_base.h
 include/seqan/index/index_bwt.h
 include/seqan/index/index_childtab.h
+include/seqan/index/index_device.h
 include/seqan/index/index_dfi.h
 include/seqan/index/index_esa_algs.h
 include/seqan/index/index_esa_algs_multi.h
 include/seqan/index/index_esa_base.h
 include/seqan/index/index_esa_drawing.h
 include/seqan/index/index_esa_stree.h
-include/seqan/index/index_generated_forwards.h
+include/seqan/index/index_fm.h
+include/seqan/index/index_fm_compressed_sa.h
+include/seqan/index/index_fm_compressed_sa_iterator.h
+include/seqan/index/index_fm_device.h
+include/seqan/index/index_fm_dox.h
+include/seqan/index/index_fm_lf_table.h
+include/seqan/index/index_fm_rank_dictionary_base.h
+include/seqan/index/index_fm_rank_dictionary_levels.h
+include/seqan/index/index_fm_rank_dictionary_naive.h
+include/seqan/index/index_fm_rank_dictionary_wt.h
+include/seqan/index/index_fm_right_array_binary_tree.h
+include/seqan/index/index_fm_right_array_binary_tree_iterator.h
+include/seqan/index/index_fm_sparse_string.h
+include/seqan/index/index_fm_stree.h
+include/seqan/index/index_forwards.h
 include/seqan/index/index_lcp.h
 include/seqan/index/index_lcp_tree.h
-include/seqan/index/index_manual_forwards.h
 include/seqan/index/index_pizzachili.h
 include/seqan/index/index_pizzachili_find.h
 include/seqan/index/index_pizzachili_string.h
 include/seqan/index/index_qgram.h
+include/seqan/index/index_qgram_bucketrefinement.h
 include/seqan/index/index_qgram_openaddressing.h
+include/seqan/index/index_qgram_stree.h
 include/seqan/index/index_sa_btree.h
 include/seqan/index/index_sa_bwtwalk.h
 include/seqan/index/index_sa_lss.h
 include/seqan/index/index_sa_mm.h
 include/seqan/index/index_sa_qsort.h
+include/seqan/index/index_sa_stree.h
+include/seqan/index/index_sa_truncated.h
 include/seqan/index/index_shawarma.h
 include/seqan/index/index_shims.h
 include/seqan/index/index_skew3.h
 include/seqan/index/index_skew7.h
 include/seqan/index/index_skew7_multi.h
+include/seqan/index/index_view.h
 include/seqan/index/index_wotd.h
 include/seqan/index/pipe_merger3.h
 include/seqan/index/pipe_merger7.h
@@ -316,48 +394,99 @@ include/seqan/index/radix.h
 include/seqan/index/repeat_base.h
 include/seqan/index/shape_base.h
 include/seqan/index/shape_gapped.h
+include/seqan/index/shape_minimizer.h
 include/seqan/index/shape_onegapped.h
 include/seqan/index/shape_predefined.h
 include/seqan/index/shape_threshold.h
+include/seqan/journaled_set.h
+include/seqan/journaled_set/journal_alignment_interface.h
+include/seqan/journaled_set/journal_alignment_traceback_adaptor.h
+include/seqan/journaled_set/journaled_set_base.h
+include/seqan/journaled_set/journaled_set_impl.h
+include/seqan/journaled_set/journaled_set_join.h
+include/seqan/journaled_set/journaled_set_join_config.h
+include/seqan/journaled_set/journaled_set_join_global_align_compact.h
+include/seqan/journaled_set/journaled_set_join_global_align_manhatten.h
+include/seqan/journaled_set/journaled_set_journal_trace_descriptor.h
+include/seqan/journaled_set/score_biaffine.h
+include/seqan/journaled_string_tree.h
+include/seqan/journaled_string_tree/delta_map.h
+include/seqan/journaled_string_tree/delta_map_entry.h
+include/seqan/journaled_string_tree/delta_map_iterator.h
+include/seqan/journaled_string_tree/delta_store.h
+include/seqan/journaled_string_tree/journaled_string_tree_base.h
+include/seqan/journaled_string_tree/journaled_string_tree_impl.h
+include/seqan/journaled_string_tree/journaled_string_tree_sequence_buffer.h
+include/seqan/journaled_string_tree/journaled_string_tree_traverser.h
+include/seqan/journaled_string_tree/journaled_string_tree_traverser_node.h
+include/seqan/journaled_string_tree/journaled_string_tree_traverser_util.h
+include/seqan/journaled_string_tree/jst_extension_base.h
+include/seqan/journaled_string_tree/jst_extension_horspool.h
+include/seqan/journaled_string_tree/jst_extension_myers_ukkonen.h
+include/seqan/journaled_string_tree/jst_extension_shiftand.h
+include/seqan/journaled_string_tree/jst_extension_shiftor.h
+include/seqan/journaled_string_tree/observable.h
+include/seqan/journaled_string_tree/stack_observer.h
 include/seqan/map.h
 include/seqan/map/map_adapter_stl.h
 include/seqan/map/map_base.h
 include/seqan/map/map_chooser.h
-include/seqan/map/map_generated_forwards.h
 include/seqan/map/map_skiplist.h
 include/seqan/map/map_vector.h
 include/seqan/map/sumlist.h
 include/seqan/map/sumlist_mini.h
 include/seqan/map/sumlist_skip.h
+include/seqan/math.h
+include/seqan/math/math_common_factor.h
+include/seqan/math/math_operators.h
+include/seqan/math/math_rational.h
+include/seqan/misc/accumulators.h
+include/seqan/misc/base.h
+include/seqan/misc/bit_twiddling.h
+include/seqan/misc/bit_twiddling_functors.h
+include/seqan/misc/cuda.h
+include/seqan/misc/dequeue.h
 include/seqan/misc/edit_environment.h
-include/seqan/misc/misc_base.h
-include/seqan/misc/misc_cmdparser.h
-include/seqan/misc/misc_dequeue.h
-include/seqan/misc/misc_generated_forwards.h
-include/seqan/misc/misc_interval_tree.h
-include/seqan/misc/misc_long_word.h
-include/seqan/misc/misc_map.h
-include/seqan/misc/misc_parsing.h
-include/seqan/misc/misc_random.h
-include/seqan/misc/misc_set.h
-include/seqan/misc/misc_svg.h
+include/seqan/misc/interval_tree.h
+include/seqan/misc/map.h
+include/seqan/misc/memset.h
+include/seqan/misc/name_store_cache.h
 include/seqan/misc/priority_type_base.h
 include/seqan/misc/priority_type_heap.h
+include/seqan/misc/set.h
+include/seqan/misc/svg.h
+include/seqan/misc/terminal.h
+include/seqan/misc/union_find.h
 include/seqan/modifier.h
+include/seqan/modifier/cyclic_shape.h
 include/seqan/modifier/modifier_alphabet.h
 include/seqan/modifier/modifier_alphabet_expansion.h
+include/seqan/modifier/modifier_cyclic_shape.h
 include/seqan/modifier/modifier_functors.h
-include/seqan/modifier/modifier_generated_forwards.h
 include/seqan/modifier/modifier_iterator.h
+include/seqan/modifier/modifier_position.h
 include/seqan/modifier/modifier_reverse.h
 include/seqan/modifier/modifier_shortcuts.h
 include/seqan/modifier/modifier_string.h
 include/seqan/modifier/modifier_view.h
 include/seqan/parallel.h
+include/seqan/parallel/parallel_algorithms.h
 include/seqan/parallel/parallel_atomic_misc.h
 include/seqan/parallel/parallel_atomic_primitives.h
-include/seqan/parallel/parallel_generated_forwards.h
+include/seqan/parallel/parallel_lock.h
 include/seqan/parallel/parallel_macros.h
+include/seqan/parallel/parallel_queue.h
+include/seqan/parallel/parallel_queue_suspendable.h
+include/seqan/parallel/parallel_resource_pool.h
+include/seqan/parallel/parallel_sequence.h
+include/seqan/parallel/parallel_serializer.h
+include/seqan/parallel/parallel_splitting.h
+include/seqan/parallel/parallel_tags.h
+include/seqan/parse_lm.h
+include/seqan/parse_lm/local_match_store.h
+include/seqan/parse_lm/parse_blastn_tabular.h
+include/seqan/parse_lm/parse_lastz_general.h
+include/seqan/parse_lm/parse_stellar_gff.h
 include/seqan/pipe.h
 include/seqan/pipe/pipe_base.h
 include/seqan/pipe/pipe_caster.h
@@ -365,7 +494,6 @@ include/seqan/pipe/pipe_counter.h
 include/seqan/pipe/pipe_echoer.h
 include/seqan/pipe/pipe_edit_environment.h
 include/seqan/pipe/pipe_filter.h
-include/seqan/pipe/pipe_generated_forwards.h
 include/seqan/pipe/pipe_iterator.h
 include/seqan/pipe/pipe_joiner.h
 include/seqan/pipe/pipe_namer.h
@@ -378,118 +506,109 @@ include/seqan/pipe/pool_mapper.h
 include/seqan/pipe/pool_sorter.h
 include/seqan/platform.h
 include/seqan/platform/platform_gcc.h
-include/seqan/platform/platform_generated_forwards.h
-include/seqan/platform/platform_mingw.h
-include/seqan/platform/platform_solaris.h
+include/seqan/platform/platform_icc.h
+include/seqan/platform/platform_nvcc.h
 include/seqan/platform/platform_windows.h
 include/seqan/random.h
-include/seqan/random/ext_MersenneTwister.h
 include/seqan/random/random_base.h
-include/seqan/random/random_generated_forwards.h
-include/seqan/random/random_geometric.h
-include/seqan/random/random_lognormal.h
-include/seqan/random/random_mt19937.h
-include/seqan/random/random_normal.h
-include/seqan/random/random_rng_functor.h
-include/seqan/random/random_shuffle.h
-include/seqan/random/random_uniform.h
-include/seqan/refinement.h
-include/seqan/refinement/graph_algorithm_refine_align.h
-include/seqan/refinement/graph_algorithm_refine_aligngraph.h
-include/seqan/refinement/graph_algorithm_refine_annotation.h
-include/seqan/refinement/graph_algorithm_refine_exact.h
-include/seqan/refinement/graph_algorithm_refine_exact_iterative.h
-include/seqan/refinement/graph_algorithm_refine_fragment.h
-include/seqan/refinement/graph_algorithm_refine_inexact.h
-include/seqan/refinement/graph_algorithm_refine_scoring.h
-include/seqan/refinement/graph_impl_align.h
-include/seqan/refinement/graph_impl_align_adapt.h
-include/seqan/refinement/refinement_generated_forwards.h
+include/seqan/random/random_beta.h
+include/seqan/random/random_util.h
+include/seqan/realign.h
+include/seqan/realign/realign_base.h
+include/seqan/realign/realign_helper_functions.h
+include/seqan/reduced_aminoacid.h
+include/seqan/reduced_aminoacid/reduced_aminoacid_base.h
+include/seqan/reduced_aminoacid/reduced_aminoacid_base_late.h
+include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_base.h
+include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h
+include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h
+include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h
+include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_base.h
+include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_tables.h
+include/seqan/roi_io.h
+include/seqan/roi_io/read_roi.h
+include/seqan/roi_io/roi_file.h
+include/seqan/roi_io/roi_io_context.h
+include/seqan/roi_io/roi_record.h
+include/seqan/roi_io/write_roi.h
 include/seqan/score.h
 include/seqan/score/score_base.h
 include/seqan/score/score_edit.h
-include/seqan/score/score_generated_forwards.h
 include/seqan/score/score_matrix.h
 include/seqan/score/score_matrix_data.h
+include/seqan/score/score_matrix_io.h
 include/seqan/score/score_simple.h
 include/seqan/seeds.h
-include/seqan/seeds/banded_align.h
-include/seqan/seeds/banded_chain_align.h
-include/seqan/seeds/banded_chain_align_affine.h
-include/seqan/seeds/global_seed_chain.h
-include/seqan/seeds/memoryManager_base.h
-include/seqan/seeds/memoryManager_int.h
-include/seqan/seeds/propertyMap.h
-include/seqan/seeds/seedHandlingTags.h
-include/seqan/seeds/seedSet_base.h
-include/seqan/seeds/seedSet_iterator.h
-include/seqan/seeds/seedSet_score.h
-include/seqan/seeds/seed_base.h
-include/seqan/seeds/seed_multi.h
-include/seqan/seeds/seeds_generated_forwards.h
-include/seqan/seeds2.h
-include/seqan/seeds2/align_chain_banded.h
-include/seqan/seeds2/align_dynprog_affine.h
-include/seqan/seeds2/align_dynprog_banded_affine.h
-include/seqan/seeds2/align_dynprog_banded_linear.h
-include/seqan/seeds2/align_dynprog_linear.h
-include/seqan/seeds2/basic_iter_indirect.h
-include/seqan/seeds2/seeds2_generated_forwards.h
-include/seqan/seeds2/seeds_base.h
-include/seqan/seeds2/seeds_combination.h
-include/seqan/seeds2/seeds_extension.h
-include/seqan/seeds2/seeds_global_chaining.h
-include/seqan/seeds2/seeds_global_chaining_base.h
-include/seqan/seeds2/seeds_global_chaining_gusfield.h
-include/seqan/seeds2/seeds_seed_base.h
-include/seqan/seeds2/seeds_seed_chained.h
-include/seqan/seeds2/seeds_seed_diagonal.h
-include/seqan/seeds2/seeds_seed_set_base.h
-include/seqan/seeds2/seeds_seed_set_non_scored.h
-include/seqan/seeds2/seeds_seed_set_scored.h
-include/seqan/seeds2/seeds_seed_set_unordered.h
-include/seqan/seeds2/seeds_seed_simple.h
+include/seqan/seeds/banded_chain_alignment.h
+include/seqan/seeds/banded_chain_alignment_impl.h
+include/seqan/seeds/banded_chain_alignment_profile.h
+include/seqan/seeds/banded_chain_alignment_scout.h
+include/seqan/seeds/banded_chain_alignment_traceback.h
+include/seqan/seeds/basic_iter_indirect.h
+include/seqan/seeds/seeds_base.h
+include/seqan/seeds/seeds_combination.h
+include/seqan/seeds/seeds_extension.h
+include/seqan/seeds/seeds_global_chaining.h
+include/seqan/seeds/seeds_global_chaining_base.h
+include/seqan/seeds/seeds_global_chaining_gusfield.h
+include/seqan/seeds/seeds_seed_base.h
+include/seqan/seeds/seeds_seed_chained.h
+include/seqan/seeds/seeds_seed_diagonal.h
+include/seqan/seeds/seeds_seed_set_base.h
+include/seqan/seeds/seeds_seed_set_non_scored.h
+include/seqan/seeds/seeds_seed_set_scored.h
+include/seqan/seeds/seeds_seed_set_unordered.h
+include/seqan/seeds/seeds_seed_simple.h
+include/seqan/seq_io.h
+include/seqan/seq_io/fai_index.h
+include/seqan/seq_io/fasta_fastq.h
+include/seqan/seq_io/genomic_region.h
+include/seqan/seq_io/read_embl.h
+include/seqan/seq_io/read_genbank.h
+include/seqan/seq_io/sequence_file.h
 include/seqan/sequence.h
 include/seqan/sequence/adapt_array_pointer.h
-include/seqan/sequence/adapt_std_list.h
-include/seqan/sequence/adapt_std_string.h
-include/seqan/sequence/adapt_std_vector.h
+include/seqan/sequence/adapt_stl_container.h
+include/seqan/sequence/adapt_thrust_vector.h
+include/seqan/sequence/container_view.h
+include/seqan/sequence/container_view_zip.h
 include/seqan/sequence/iter_concat_virtual.h
 include/seqan/sequence/segment_base.h
 include/seqan/sequence/segment_infix.h
 include/seqan/sequence/segment_prefix.h
 include/seqan/sequence/segment_suffix.h
+include/seqan/sequence/segment_utils.h
 include/seqan/sequence/sequence_concatenator.h
 include/seqan/sequence/sequence_forwards.h
-include/seqan/sequence/sequence_generated_forwards.h
 include/seqan/sequence/sequence_interface.h
 include/seqan/sequence/sequence_lexical.h
 include/seqan/sequence/sequence_shortcuts.h
-include/seqan/sequence/sequence_stream.h
 include/seqan/sequence/string_alloc.h
 include/seqan/sequence/string_array.h
 include/seqan/sequence/string_base.h
 include/seqan/sequence/string_block.h
 include/seqan/sequence/string_cstyle.h
 include/seqan/sequence/string_packed.h
+include/seqan/sequence/string_packed_old.h
 include/seqan/sequence/string_set_base.h
 include/seqan/sequence/string_set_concat_direct.h
 include/seqan/sequence/string_set_dependent_generous.h
 include/seqan/sequence/string_set_dependent_tight.h
+include/seqan/sequence/string_set_device.h
 include/seqan/sequence/string_set_owner.h
+include/seqan/sequence/string_set_segment.h
+include/seqan/sequence/string_set_view.h
 include/seqan/sequence_journaled.h
 include/seqan/sequence_journaled/journal_entries_sorted_array.h
-include/seqan/sequence_journaled/journal_entries_unbalanced_tree.h
-include/seqan/sequence_journaled/journal_entries_unbalanced_tree_iterator.h
-include/seqan/sequence_journaled/journal_entries_unbalanced_tree_node.h
 include/seqan/sequence_journaled/journal_entry.h
 include/seqan/sequence_journaled/sequence_journaled.h
-include/seqan/sequence_journaled/sequence_journaled_forwards.h
-include/seqan/sequence_journaled/sequence_journaled_generated_forwards.h
 include/seqan/sequence_journaled/sequence_journaled_iterator.h
+include/seqan/sequence_journaled/sequence_journaled_iterator_fast.h
+include/seqan/simple_intervals_io.h
+include/seqan/simple_intervals_io/simple_intervals_file.h
+include/seqan/simple_intervals_io/simple_intervals_io.h
 include/seqan/statistics.h
 include/seqan/statistics/statistics_base.h
-include/seqan/statistics/statistics_generated_forwards.h
 include/seqan/statistics/statistics_markov_model.h
 include/seqan/store.h
 include/seqan/store/store_align.h
@@ -498,1614 +617,1285 @@ include/seqan/store/store_all.h
 include/seqan/store/store_annotation.h
 include/seqan/store/store_base.h
 include/seqan/store/store_contig.h
-include/seqan/store/store_generated_forwards.h
 include/seqan/store/store_intervaltree.h
 include/seqan/store/store_io.h
-include/seqan/store/store_io_bam.h
 include/seqan/store/store_io_gff.h
 include/seqan/store/store_io_sam.h
 include/seqan/store/store_io_ucsc.h
 include/seqan/store/store_library.h
 include/seqan/store/store_matepair.h
 include/seqan/store/store_read.h
+include/seqan/stream.h
+include/seqan/stream/adapt_ios.h
+include/seqan/stream/buffered_stream.h
+include/seqan/stream/file_stream.h
+include/seqan/stream/formatted_file.h
+include/seqan/stream/guess_format.h
+include/seqan/stream/iostream_bgzf.h
+include/seqan/stream/iostream_bzip2.h
+include/seqan/stream/iostream_bzip2_impl.h
+include/seqan/stream/iostream_zip.h
+include/seqan/stream/iostream_zip_impl.h
+include/seqan/stream/iostream_zutil.h
+include/seqan/stream/iter_stream.h
+include/seqan/stream/lexical_cast.h
+include/seqan/stream/stream_base.h
+include/seqan/stream/stream_compressor.h
+include/seqan/stream/tokenization.h
+include/seqan/stream/virtual_stream.h
 include/seqan/system.h
 include/seqan/system/file_async.h
 include/seqan/system/file_directory.h
-include/seqan/system/file_manual_forwards.h
+include/seqan/system/file_forwards.h
 include/seqan/system/file_sync.h
 include/seqan/system/system_base.h
+include/seqan/system/system_condition.h
+include/seqan/system/system_critical_section.h
 include/seqan/system/system_event.h
-include/seqan/system/system_generated_forwards.h
-include/seqan/system/system_manual_forwards.h
+include/seqan/system/system_forwards.h
 include/seqan/system/system_mutex.h
-include/seqan/system/system_sema.h
 include/seqan/system/system_thread.h
+include/seqan/tabix_io.h
+include/seqan/tabix_io/tabix_index_tbi.h
+include/seqan/translation.h
+include/seqan/translation/translation.h
+include/seqan/translation/translation_tables.h
+include/seqan/ucsc_io.h
+include/seqan/ucsc_io/ucsc_file.h
+include/seqan/ucsc_io/ucsc_io.h
+include/seqan/ucsc_io/ucsc_record.h
+include/seqan/vcf_io.h
+include/seqan/vcf_io/read_vcf.h
+include/seqan/vcf_io/vcf_file.h
+include/seqan/vcf_io/vcf_header.h
+include/seqan/vcf_io/vcf_header_record.h
+include/seqan/vcf_io/vcf_io_context.h
+include/seqan/vcf_io/vcf_record.h
+include/seqan/vcf_io/write_vcf.h
 include/seqan/version.h
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+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PigeonholePattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PizzaChiliIndex.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PizzaChiliString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PoolConfig.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PoolConfigSize.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PoolSpec.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PositionIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PrefixSegment.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PriorityHeap.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ProfileSeqFracScore.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ProfileSeqScore.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ReducedAminoAcid.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ResizableContainerView.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_RightArrayBinaryTreeIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Rna.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Rna5.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_RoiFileIn.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_RoiFileOut.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Sampler.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SeqFileIn.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SeqFileOut.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SetHorspoolPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ShiftAndPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ShiftOrPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Shifter.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimpleAllocator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimpleHolder.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimpleIntervalsFileIn.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimpleIntervalsFileInOut.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimplePattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimpleScore.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimpleSeed.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimpleShape.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SinglePoolAllocator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Skiplist.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SorterConfig.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SorterConfigSize.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SorterSpec.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Source.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_StdAdaptorIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_StoreIntervalsIntervalTreeNode.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_StorePointsOnlyIntervalTreeNode.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_StreamIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SuffixSegment.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SuperMaxRepeatsFastIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SuperMaxRepeatsIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SwiftFinder.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SwiftLocalFinder.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SwiftLocalPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SwiftPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SwiftSemiGlobalFinder.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SwiftSemiGlobalPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SyncFile.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_TightDependentStringSet.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_TopDownHistoryIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_TopDownIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Tree.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_TrieBfamPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_TristateHolder.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Tupler.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_TwoLevelRankDictionary.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_UcscFileIn.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_UcscFileOut.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_UnbandedLocalAlignmentEnumerator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_UndirectedGraph.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_UnexpectedEnd.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_UngappedShape.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_VSTreeIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_VcfFileIn.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_VcfFileOut.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_VectorSet.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_VertexIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_WaveletTree.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_WildShiftAndPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_WordGraph.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_WuManberPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ZipContainerView.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ZipIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/tag_Default.html
+%%PORTDOCS%%%%DOCSDIR%%/html/tag_DotDrawing.html
+%%PORTDOCS%%%%DOCSDIR%%/html/tag_EditDistance.html
+%%PORTDOCS%%%%DOCSDIR%%/html/tag_GeneticCode.html
+%%PORTDOCS%%%%DOCSDIR%%/html/tag_HammingDistance.html
+%%PORTDOCS%%%%DOCSDIR%%/html/tag_LevenshteinDistance.html
+%%PORTDOCS%%%%DOCSDIR%%/html/tag_Move.html
+%%PORTDOCS%%%%DOCSDIR%%/html/tag_Murphy10.html
+%%PORTDOCS%%%%DOCSDIR%%/html/tag_Nothing.html
+%%PORTDOCS%%%%DOCSDIR%%/html/variable_BAM_95FLAG_95SUPPLEMENTARY_32_61_320x0800.html
+%%PORTDOCS%%%%DOCSDIR%%/html/variable_LibraryStoreElementstd.html
+%%PORTDOCS%%@dir %%DOCSDIR%%/html/docs/seqan
+%%PORTDOCS%%@dir %%DOCSDIR%%/html/lists
diff --git a/biology/seqan1/Makefile b/biology/seqan1/Makefile
new file mode 100644
index 000000000000..d5222cac07b2
--- /dev/null
+++ b/biology/seqan1/Makefile
@@ -0,0 +1,31 @@
+# Created by: h2
+# $FreeBSD$
+
+PORTNAME=	seqan
+PORTVERSION=	1.3.1
+PORTREVISION=	3
+CATEGORIES=	biology
+MASTER_SITES=	http://ftp.seqan.de/releases/
+PKGNAMESUFFIX=	1
+
+MAINTAINER=	h2+fbsdports@fsfe.org
+COMMENT=	C++ Sequence Analysis Library
+
+LICENSE=	BSD3CLAUSE
+LICENSE_FILE_BSD=${WRKSRC}/seqan/LICENSE
+
+USES=		zip
+NO_BUILD=	yes
+
+CONFLICTS=	seqan-[2-9]*
+
+do-install:
+	${MKDIR} ${STAGEDIR}/${PREFIX}/include/${PORTNAME}
+	cd ${WRKSRC} && ${COPYTREE_SHARE} ./${PORTNAME} ${STAGEDIR}/${PREFIX}/include
+	cd ${WRKSRC} && ${INSTALL_DATA} ./${PORTNAME}.h ${STAGEDIR}/${PREFIX}/include
+
+post-install:
+	${MKDIR} ${STAGEDIR}${DOCSDIR}
+	cd ${WRKSRC}/docs && ${COPYTREE_SHARE} ./ ${STAGEDIR}${DOCSDIR}
+
+.include <bsd.port.mk>
diff --git a/biology/seqan1/distinfo b/biology/seqan1/distinfo
new file mode 100644
index 000000000000..3e7a0a49d7b4
--- /dev/null
+++ b/biology/seqan1/distinfo
@@ -0,0 +1,2 @@
+SHA256 (seqan-1.3.1.zip) = 87eebe73ace9ada2f4664a768ae212d4acc5fb3ce87702709c3d15bf2d153aeb
+SIZE (seqan-1.3.1.zip) = 8787521
diff --git a/biology/seqan1/pkg-descr b/biology/seqan1/pkg-descr
new file mode 100644
index 000000000000..5f27809a1ba8
--- /dev/null
+++ b/biology/seqan1/pkg-descr
@@ -0,0 +1,10 @@
+SeqAn is an open source C++ library of efficient algorithms
+and data structures for the analysis of sequences with the
+focus on biological data.
+
+This port includes only the library, the apps have been
+moved to biology/seqan-apps. This is the last release of
+the version 1 API, it is highly recommended to upgrade to 
+biology/seqan (version 2).
+
+WWW: http://www.seqan.de/
diff --git a/biology/seqan1/pkg-plist b/biology/seqan1/pkg-plist
new file mode 100644
index 000000000000..e6c2faed81f0
--- /dev/null
+++ b/biology/seqan1/pkg-plist
@@ -0,0 +1,1983 @@
+include/seqan.h
+include/seqan/LICENSE
+include/seqan/align.h
+include/seqan/align/align_algorithms.h
+include/seqan/align/align_base.h
+include/seqan/align/align_cols_base.h
+include/seqan/align/align_dynprog.h
+include/seqan/align/align_generated_forwards.h
+include/seqan/align/align_hirschberg.h
+include/seqan/align/align_iterator_base.h
+include/seqan/align/align_local_dynprog.h
+include/seqan/align/align_local_dynprog_banded.h
+include/seqan/align/align_myers.h
+include/seqan/align/align_trace.h
+include/seqan/align/gaps_array.h
+include/seqan/align/gaps_base.h
+include/seqan/align/gaps_iterator_base.h
+include/seqan/align/gaps_sumlist.h
+include/seqan/align/hirschberg_set.h
+include/seqan/align/matrix_base.h
+include/seqan/basic.h
+include/seqan/basic/basic_aggregates.h
+include/seqan/basic/basic_allocator_chunkpool.h
+include/seqan/basic/basic_allocator_interface.h
+include/seqan/basic/basic_allocator_multipool.h
+include/seqan/basic/basic_allocator_simple.h
+include/seqan/basic/basic_allocator_singlepool.h
+include/seqan/basic/basic_allocator_to_std.h
+include/seqan/basic/basic_alphabet_interface.h
+include/seqan/basic/basic_alphabet_interface2.h
+include/seqan/basic/basic_alphabet_simple.h
+include/seqan/basic/basic_alphabet_simple_tabs.h
+include/seqan/basic/basic_alphabet_trait_basic.h
+include/seqan/basic/basic_compare.h
+include/seqan/basic/basic_converter.h
+include/seqan/basic/basic_counted_ptr.h
+include/seqan/basic/basic_debug.h
+include/seqan/basic/basic_definition.h
+include/seqan/basic/basic_forwards.h
+include/seqan/basic/basic_generated_forwards.h
+include/seqan/basic/basic_holder.h
+include/seqan/basic/basic_holder_dynamic.h
+include/seqan/basic/basic_host.h
+include/seqan/basic/basic_iterator.h
+include/seqan/basic/basic_iterator_adapt_std.h
+include/seqan/basic/basic_iterator_adaptor.h
+include/seqan/basic/basic_iterator_base.h
+include/seqan/basic/basic_iterator_position.h
+include/seqan/basic/basic_iterator_simple.h
+include/seqan/basic/basic_logvalue.h
+include/seqan/basic/basic_metaprogramming.h
+include/seqan/basic/basic_operator.h
+include/seqan/basic/basic_parallelism.h
+include/seqan/basic/basic_pointer.h
+include/seqan/basic/basic_profchar.h
+include/seqan/basic/basic_profile.h
+include/seqan/basic/basic_proxy.h
+include/seqan/basic/basic_sse2.h
+include/seqan/basic/basic_tag.h
+include/seqan/basic/basic_testing.h
+include/seqan/basic/basic_transport.h
+include/seqan/basic/basic_type.h
+include/seqan/basic/basic_volatile_ptr.h
+include/seqan/blast.h
+include/seqan/blast/blast_base.h
+include/seqan/blast/blast_generated_forwards.h
+include/seqan/blast/blast_hit.h
+include/seqan/blast/blast_hit_iterator.h
+include/seqan/blast/blast_hsp.h
+include/seqan/blast/blast_hsp_iterator.h
+include/seqan/blast/blast_iterator.h
+include/seqan/blast/blast_parsing.h
+include/seqan/blast/blast_report.h
+include/seqan/blast/blast_run.h
+include/seqan/blast/blast_stream_hit.h
+include/seqan/blast/blast_stream_hit_iterator.h
+include/seqan/blast/blast_stream_hsp_iterator.h
+include/seqan/blast/blast_stream_report.h
+include/seqan/chaining.h
+include/seqan/chaining/chain_base.h
+include/seqan/chaining/chain_generic.h
+include/seqan/chaining/chain_meta_fragment.h
+include/seqan/chaining/chain_point.h
+include/seqan/chaining/chain_wrapper_point.h
+include/seqan/chaining/chaining_generated_forwards.h
+include/seqan/chaining/fragment.h
+include/seqan/chaining/geom_distribution.h
+include/seqan/chaining/range_max_tree.h
+include/seqan/chaining/range_tree.h
+include/seqan/chaining/rmt_base.h
+include/seqan/chaining/rmt_common_algos.h
+include/seqan/chaining/rmt_compl_algos.h
+include/seqan/chaining/rmt_def_algos.h
+include/seqan/chaining/rmt_skip_base_element.h
+include/seqan/chaining/rmt_skip_element.h
+include/seqan/chaining/rt_base.h
+include/seqan/chaining/rt_common_algos.h
+include/seqan/chaining/rt_impl.h
+include/seqan/chaining/rt_skip_base_element.h
+include/seqan/chaining/rt_skip_element.h
+include/seqan/chaining/rt_sl_base.h
+include/seqan/chaining/rt_sl_compl_algos.h
+include/seqan/chaining/rt_sl_def_algos.h
+include/seqan/chaining/rt_sl_impl.h
+include/seqan/chaining/score_chain.h
+include/seqan/chaining/score_chain_sop.h
+include/seqan/chaining/score_manhattan.h
+include/seqan/chaining/score_zero.h
+include/seqan/chaining/skip_base_element.h
+include/seqan/chaining/skip_element.h
+include/seqan/chaining/skip_list.h
+include/seqan/chaining/skip_list_base.h
+include/seqan/chaining/skip_list_dynamic.h
+include/seqan/chaining/skip_list_impl.h
+include/seqan/chaining/skip_list_iterator.h
+include/seqan/chaining/skip_list_type.h
+include/seqan/chaining/skip_pool_alloc.h
+include/seqan/chaining/tree_chain.h
+include/seqan/chaining/tree_chain_sop.h
+include/seqan/chaining/tree_chain_utils.h
+include/seqan/consensus.h
+include/seqan/consensus/consensus_base.h
+include/seqan/consensus/consensus_generated_forwards.h
+include/seqan/consensus/consensus_library.h
+include/seqan/consensus/consensus_realign.h
+include/seqan/consensus/consensus_score.h
+include/seqan/file.h
+include/seqan/file/chunk_collector.h
+include/seqan/file/cstream.h
+include/seqan/file/file_array.h
+include/seqan/file/file_base.h
+include/seqan/file/file_cstyle.h
+include/seqan/file/file_filereader.h
+include/seqan/file/file_filereaderiterator.h
+include/seqan/file/file_format.h
+include/seqan/file/file_format_cgviz.h
+include/seqan/file/file_format_embl.h
+include/seqan/file/file_format_fasta.h
+include/seqan/file/file_format_fasta_align.h
+include/seqan/file/file_format_genbank.h
+include/seqan/file/file_format_guess.h
+include/seqan/file/file_format_mmap.h
+include/seqan/file/file_format_raw.h
+include/seqan/file/file_forwards.h
+include/seqan/file/file_generated_forwards.h
+include/seqan/file/file_page.h
+include/seqan/file/file_page_raid0.h
+include/seqan/file/meta.h
+include/seqan/file/stream.h
+include/seqan/file/stream_algorithms.h
+include/seqan/file/string_external.h
+include/seqan/file/string_mmap.h
+include/seqan/find.h
+include/seqan/find/find_abndm.h
+include/seqan/find/find_ahocorasick.h
+include/seqan/find/find_base.h
+include/seqan/find/find_begin.h
+include/seqan/find/find_bndm.h
+include/seqan/find/find_bom.h
+include/seqan/find/find_generated_forwards.h
+include/seqan/find/find_hamming_simple.h
+include/seqan/find/find_horspool.h
+include/seqan/find/find_multi.h
+include/seqan/find/find_multiple_bfam.h
+include/seqan/find/find_multiple_shiftand.h
+include/seqan/find/find_myers_ukkonen.h
+include/seqan/find/find_pattern_base.h
+include/seqan/find/find_pex.h
+include/seqan/find/find_score.h
+include/seqan/find/find_set_horspool.h
+include/seqan/find/find_shiftand.h
+include/seqan/find/find_shiftor.h
+include/seqan/find/find_simple.h
+include/seqan/find/find_wild_shiftand.h
+include/seqan/find/find_wumanber.h
+include/seqan/find2.h
+include/seqan/find2/find2_generated_forwards.h
+include/seqan/find2/find_approx_dpsearch.h
+include/seqan/find2/find_approx_find_begin.h
+include/seqan/find2/find_base.h
+include/seqan/find2/find_exact_shiftand.h
+include/seqan/find2/find_exact_simple.h
+include/seqan/find2/find_finder_default.h
+include/seqan/find2/find_hamming_simple.h
+include/seqan/find2/find_multiple_exact_simple.h
+include/seqan/find2/find_pattern_wild_shiftand.h
+include/seqan/find_motif.h
+include/seqan/find_motif/em_algorithm.h
+include/seqan/find_motif/find_motif_base.h
+include/seqan/find_motif/find_motif_epatternbranching.h
+include/seqan/find_motif/find_motif_generated_forwards.h
+include/seqan/find_motif/find_motif_pms1.h
+include/seqan/find_motif/find_motif_pmsp.h
+include/seqan/find_motif/find_motif_projection.h
+include/seqan/find_motif/frequency_distribution.h
+include/seqan/find_motif/profile.h
+include/seqan/find_motif/pseudocount_base.h
+include/seqan/find_motif/pseudocount_mode_c.h
+include/seqan/find_motif/pseudocount_mode_p.h
+include/seqan/find_motif/sequence_model_types.h
+include/seqan/graph_algorithms.h
+include/seqan/graph_algorithms/graph_algorithm.h
+include/seqan/graph_algorithms/graph_algorithm_heap_tree.h
+include/seqan/graph_algorithms/graph_algorithm_hmm.h
+include/seqan/graph_algorithms/graph_algorithm_lis_his.h
+include/seqan/graph_algorithms/graph_algorithms_generated_forwards.h
+include/seqan/graph_align.h
+include/seqan/graph_align/graph_align_banded_gotoh.h
+include/seqan/graph_align/graph_align_banded_needleman_wunsch.h
+include/seqan/graph_align/graph_align_banded_smith_waterman_clump.h
+include/seqan/graph_align/graph_align_base.h
+include/seqan/graph_align/graph_align_config.h
+include/seqan/graph_align/graph_align_generated_forwards.h
+include/seqan/graph_align/graph_align_gotoh.h
+include/seqan/graph_align/graph_align_hirschberg.h
+include/seqan/graph_align/graph_align_interface.h
+include/seqan/graph_align/graph_align_needleman_wunsch.h
+include/seqan/graph_align/graph_align_smith_waterman.h
+include/seqan/graph_align/graph_align_smith_waterman_clump.h
+include/seqan/graph_msa.h
+include/seqan/graph_msa/graph_align_tcoffee_base.h
+include/seqan/graph_msa/graph_align_tcoffee_distance.h
+include/seqan/graph_msa/graph_align_tcoffee_guidetree.h
+include/seqan/graph_msa/graph_align_tcoffee_io.h
+include/seqan/graph_msa/graph_align_tcoffee_kmer.h
+include/seqan/graph_msa/graph_align_tcoffee_library.h
+include/seqan/graph_msa/graph_align_tcoffee_msa.h
+include/seqan/graph_msa/graph_align_tcoffee_progressive.h
+include/seqan/graph_msa/graph_align_tcoffee_refinement.h
+include/seqan/graph_msa/graph_msa_generated_forwards.h
+include/seqan/graph_types.h
+include/seqan/graph_types/graph_base.h
+include/seqan/graph_types/graph_drawing.h
+include/seqan/graph_types/graph_edgestump.h
+include/seqan/graph_types/graph_idmanager.h
+include/seqan/graph_types/graph_impl_automaton.h
+include/seqan/graph_types/graph_impl_directed.h
+include/seqan/graph_types/graph_impl_fragment.h
+include/seqan/graph_types/graph_impl_hmm.h
+include/seqan/graph_types/graph_impl_oracle.h
+include/seqan/graph_types/graph_impl_tree.h
+include/seqan/graph_types/graph_impl_trie.h
+include/seqan/graph_types/graph_impl_undirected.h
+include/seqan/graph_types/graph_impl_wordgraph.h
+include/seqan/graph_types/graph_interface.h
+include/seqan/graph_types/graph_iterator.h
+include/seqan/graph_types/graph_iterator_adjacency.h
+include/seqan/graph_types/graph_iterator_bfs.h
+include/seqan/graph_types/graph_iterator_dfs.h
+include/seqan/graph_types/graph_iterator_edge.h
+include/seqan/graph_types/graph_iterator_outedge.h
+include/seqan/graph_types/graph_iterator_vertex.h
+include/seqan/graph_types/graph_property.h
+include/seqan/graph_types/graph_types_generated_forwards.h
+include/seqan/graph_types/graph_utility_parsing.h
+include/seqan/index.h
+include/seqan/index/find_index.h
+include/seqan/index/find_index_approx.h
+include/seqan/index/find_index_esa.h
+include/seqan/index/find_index_qgram.h
+include/seqan/index/find_quasar.h
+include/seqan/index/find_swift.h
+include/seqan/index/index_base.h
+include/seqan/index/index_bwt.h
+include/seqan/index/index_childtab.h
+include/seqan/index/index_dfi.h
+include/seqan/index/index_esa_algs.h
+include/seqan/index/index_esa_algs_multi.h
+include/seqan/index/index_esa_base.h
+include/seqan/index/index_esa_drawing.h
+include/seqan/index/index_esa_stree.h
+include/seqan/index/index_generated_forwards.h
+include/seqan/index/index_lcp.h
+include/seqan/index/index_lcp_tree.h
+include/seqan/index/index_manual_forwards.h
+include/seqan/index/index_pizzachili.h
+include/seqan/index/index_pizzachili_find.h
+include/seqan/index/index_pizzachili_string.h
+include/seqan/index/index_qgram.h
+include/seqan/index/index_qgram_openaddressing.h
+include/seqan/index/index_sa_btree.h
+include/seqan/index/index_sa_bwtwalk.h
+include/seqan/index/index_sa_lss.h
+include/seqan/index/index_sa_mm.h
+include/seqan/index/index_sa_qsort.h
+include/seqan/index/index_shawarma.h
+include/seqan/index/index_shims.h
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