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Port details
seqan C++ Sequence Analysis Template Library
2.2.0 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: h2+fbsdports@fsfe.org search for ports maintained by this maintainer
Port Added: 06 Jun 2012 17:52:27
License: BSD3CLAUSE
SeqAn is an open source C++ library of efficient algorithms
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/
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (1916 items)
  1. /usr/local/share/licenses/seqan-2.2.0/catalog.mk
  2. /usr/local/share/licenses/seqan-2.2.0/LICENSE
  3. /usr/local/share/licenses/seqan-2.2.0/BSD3CLAUSE
  4. include/seqan/align.h
  5. include/seqan/align/align_base.h
  6. include/seqan/align/align_cols.h
  7. include/seqan/align/align_config.h
  8. include/seqan/align/align_interface_wrapper.h
  9. include/seqan/align/align_iterator_base.h
  10. include/seqan/align/align_metafunctions.h
  11. include/seqan/align/align_traceback.h
  12. include/seqan/align/alignment_algorithm_tags.h
  13. include/seqan/align/alignment_operations.h
  14. include/seqan/align/dp_algorithm_impl.h
  15. include/seqan/align/dp_align_simd_helper.h
  16. include/seqan/align/dp_band.h
  17. include/seqan/align/dp_cell.h
  18. include/seqan/align/dp_cell_affine.h
  19. include/seqan/align/dp_cell_dynamic.h
  20. include/seqan/align/dp_cell_linear.h
  21. include/seqan/align/dp_context.h
  22. include/seqan/align/dp_formula.h
  23. include/seqan/align/dp_formula_affine.h
  24. include/seqan/align/dp_formula_dynamic.h
  25. include/seqan/align/dp_formula_linear.h
  26. include/seqan/align/dp_matrix.h
  27. include/seqan/align/dp_matrix_navigator.h
  28. include/seqan/align/dp_matrix_navigator_score_matrix.h
  29. include/seqan/align/dp_matrix_navigator_score_matrix_sparse.h
  30. include/seqan/align/dp_matrix_navigator_trace_matrix.h
  31. include/seqan/align/dp_matrix_sparse.h
  32. include/seqan/align/dp_meta_info.h
  33. include/seqan/align/dp_profile.h
  34. include/seqan/align/dp_scout.h
  35. include/seqan/align/dp_scout_simd.h
  36. include/seqan/align/dp_setup.h
  37. include/seqan/align/dp_trace_segment.h
  38. include/seqan/align/dp_traceback_adaptor.h
  39. include/seqan/align/dp_traceback_impl.h
  40. include/seqan/align/evaluate_alignment.h
  41. include/seqan/align/fragment.h
  42. include/seqan/align/gap_anchor.h
  43. include/seqan/align/gapped_value_type.h
  44. include/seqan/align/gaps_anchor.h
  45. include/seqan/align/gaps_array.h
  46. include/seqan/align/gaps_base.h
  47. include/seqan/align/gaps_iterator_anchor.h
  48. include/seqan/align/gaps_iterator_array.h
  49. include/seqan/align/gaps_iterator_base.h
  50. include/seqan/align/global_alignment_banded.h
  51. include/seqan/align/global_alignment_hirschberg_impl.h
  52. include/seqan/align/global_alignment_myers_hirschberg_impl.h
  53. include/seqan/align/global_alignment_myers_impl.h
  54. include/seqan/align/global_alignment_specialized.h
  55. include/seqan/align/global_alignment_unbanded.h
  56. include/seqan/align/local_alignment_banded.h
  57. include/seqan/align/local_alignment_banded_waterman_eggert_impl.h
  58. include/seqan/align/local_alignment_enumeration.h
  59. include/seqan/align/local_alignment_enumeration_banded.h
  60. include/seqan/align/local_alignment_enumeration_unbanded.h
  61. include/seqan/align/local_alignment_unbanded.h
  62. include/seqan/align/local_alignment_waterman_eggert_impl.h
  63. include/seqan/align/matrix_base.h
  64. include/seqan/align_extend.h
  65. include/seqan/align_extend/align_extend.h
  66. include/seqan/align_extend/align_extend_base.h
  67. include/seqan/align_extend/dp_scout_xdrop.h
  68. include/seqan/align_profile.h
  69. include/seqan/align_profile/add_to_profile.h
  70. include/seqan/align_profile/score_profile_seq.h
  71. include/seqan/align_split.h
  72. include/seqan/align_split/align_split_interface.h
  73. include/seqan/align_split/dp_scout_split.h
  74. include/seqan/alignment_free.h
  75. include/seqan/alignment_free/af_d2.h
  76. include/seqan/alignment_free/af_d2star.h
  77. include/seqan/alignment_free/af_d2z.h
  78. include/seqan/alignment_free/af_n2.h
  79. include/seqan/alignment_free/alignment_free_base.h
  80. include/seqan/alignment_free/alignment_free_comparison.h
  81. include/seqan/alignment_free/kmer_functions.h
  82. include/seqan/arg_parse.h
  83. include/seqan/arg_parse/arg_parse_argument.h
  84. include/seqan/arg_parse/arg_parse_ctd_support.h
  85. include/seqan/arg_parse/arg_parse_doc.h
  86. include/seqan/arg_parse/arg_parse_exceptions.h
  87. include/seqan/arg_parse/arg_parse_option.h
  88. include/seqan/arg_parse/arg_parse_parse.h
  89. include/seqan/arg_parse/arg_parse_type_support.h
  90. include/seqan/arg_parse/argument_parser.h
  91. include/seqan/arg_parse/tool_doc.h
  92. include/seqan/arg_parse/xml_support.h
  93. include/seqan/bam_io.h
  94. include/seqan/bam_io/bam_alignment_record.h
  95. include/seqan/bam_io/bam_alignment_record_util.h
  96. include/seqan/bam_io/bam_file.h
  97. include/seqan/bam_io/bam_header_record.h
  98. include/seqan/bam_io/bam_index_bai.h
  99. include/seqan/bam_io/bam_io_context.h
  100. include/seqan/bam_io/bam_sam_conversion.h
  101. include/seqan/bam_io/bam_scanner_cache.h
  102. include/seqan/bam_io/bam_tags_dict.h
  103. include/seqan/bam_io/cigar.h
  104. include/seqan/bam_io/read_bam.h
  105. include/seqan/bam_io/read_sam.h
  106. include/seqan/bam_io/write_bam.h
  107. include/seqan/bam_io/write_sam.h
  108. include/seqan/basic.h
  109. include/seqan/basic/aggregate_concept.h
  110. include/seqan/basic/allocator_chunkpool.h
  111. include/seqan/basic/allocator_interface.h
  112. include/seqan/basic/allocator_multipool.h
  113. include/seqan/basic/allocator_simple.h
  114. include/seqan/basic/allocator_singlepool.h
  115. include/seqan/basic/allocator_to_std.h
  116. include/seqan/basic/alphabet_adapt_builtins.h
  117. include/seqan/basic/alphabet_bio.h
  118. include/seqan/basic/alphabet_concept.h
  119. include/seqan/basic/alphabet_math.h
  120. include/seqan/basic/alphabet_profile.h
  121. include/seqan/basic/alphabet_qualities.h
  122. include/seqan/basic/alphabet_residue.h
  123. include/seqan/basic/alphabet_residue_funcs.h
  124. include/seqan/basic/alphabet_residue_tabs.h
  125. include/seqan/basic/alphabet_simple_type.h
  126. include/seqan/basic/alphabet_storage.h
  127. include/seqan/basic/array_construct_destruct.h
  128. include/seqan/basic/basic_aggregate.h
  129. include/seqan/basic/basic_allocator.h
  130. include/seqan/basic/basic_alphabet.h
  131. include/seqan/basic/basic_concept.h
  132. include/seqan/basic/basic_container.h
  133. include/seqan/basic/basic_debug.h
  134. include/seqan/basic/basic_device.h
  135. include/seqan/basic/basic_exception.h
  136. include/seqan/basic/basic_functors.h
  137. include/seqan/basic/basic_fundamental.h
  138. include/seqan/basic/basic_iterator.h
  139. include/seqan/basic/basic_math.h
  140. include/seqan/basic/basic_metaprogramming.h
  141. include/seqan/basic/basic_parallelism.h
  142. include/seqan/basic/basic_proxy.h
  143. include/seqan/basic/basic_simd_vector.h
  144. include/seqan/basic/basic_smart_pointer.h
  145. include/seqan/basic/basic_stream.h
  146. include/seqan/basic/basic_tangle.h
  147. include/seqan/basic/basic_type.h
  148. include/seqan/basic/basic_view.h
  149. include/seqan/basic/boost_preprocessor_subset.h
  150. include/seqan/basic/builtin_functions.h
  151. include/seqan/basic/concept_checking.h
  152. include/seqan/basic/container_concept.h
  153. include/seqan/basic/debug_helper.h
  154. include/seqan/basic/debug_test_system.h
  155. include/seqan/basic/fundamental_chunking.h
  156. include/seqan/basic/fundamental_comparison.h
  157. include/seqan/basic/fundamental_concepts.h
  158. include/seqan/basic/fundamental_conversion.h
  159. include/seqan/basic/fundamental_metafunctions.h
  160. include/seqan/basic/fundamental_tags.h
  161. include/seqan/basic/fundamental_transport.h
  162. include/seqan/basic/holder_base.h
  163. include/seqan/basic/holder_simple.h
  164. include/seqan/basic/holder_tristate.h
  165. include/seqan/basic/hosted_type_interface.h
  166. include/seqan/basic/iterator_adapt_pointer.h
  167. include/seqan/basic/iterator_adapt_std.h
  168. include/seqan/basic/iterator_adaptor.h
  169. include/seqan/basic/iterator_base.h
  170. include/seqan/basic/iterator_concept.h
  171. include/seqan/basic/iterator_counting.h
  172. include/seqan/basic/iterator_interface.h
  173. include/seqan/basic/iterator_position.h
  174. include/seqan/basic/iterator_range.h
  175. include/seqan/basic/iterator_zip.h
  176. include/seqan/basic/macro_deprecated.h
  177. include/seqan/basic/math_functions.h
  178. include/seqan/basic/math_log_space_value.h
  179. include/seqan/basic/metaprogramming_control.h
  180. include/seqan/basic/metaprogramming_enable_if.h
  181. include/seqan/basic/metaprogramming_logic.h
  182. include/seqan/basic/metaprogramming_math.h
  183. include/seqan/basic/metaprogramming_type.h
  184. include/seqan/basic/metaprogramming_type_algebra.h
  185. include/seqan/basic/pair_base.h
  186. include/seqan/basic/pair_bit_compressed.h
  187. include/seqan/basic/pair_packed.h
  188. include/seqan/basic/profiling.h
  189. include/seqan/basic/property_map_concept.h
  190. include/seqan/basic/proxy_base.h
  191. include/seqan/basic/proxy_iterator.h
  192. include/seqan/basic/test_system.h
  193. include/seqan/basic/triple_base.h
  194. include/seqan/basic/triple_packed.h
  195. include/seqan/basic/tuple_base.h
  196. include/seqan/basic/tuple_bit_compressed.h
  197. include/seqan/basic/volatile_ptr.h
  198. include/seqan/bed_io.h
  199. include/seqan/bed_io/bed_file.h
  200. include/seqan/bed_io/bed_record.h
  201. include/seqan/bed_io/read_bed.h
  202. include/seqan/bed_io/write_bed.h
  203. include/seqan/blast.h
  204. include/seqan/blast/blast_base.h
  205. include/seqan/blast/blast_io_context.h
  206. include/seqan/blast/blast_record.h
  207. include/seqan/blast/blast_report_out.h
  208. include/seqan/blast/blast_statistics.h
  209. include/seqan/blast/blast_tabular.h
  210. include/seqan/blast/blast_tabular_in.h
  211. include/seqan/blast/blast_tabular_lowlevel.h
  212. include/seqan/blast/blast_tabular_out.h
  213. include/seqan/consensus.h
  214. include/seqan/consensus/consensus_aligner.h
  215. include/seqan/consensus/consensus_aligner_interface.h
  216. include/seqan/consensus/consensus_alignment_options.h
  217. include/seqan/consensus/consensus_base.h
  218. include/seqan/consensus/consensus_builder.h
  219. include/seqan/consensus/consensus_library.h
  220. include/seqan/consensus/consensus_realign.h
  221. include/seqan/consensus/consensus_score.h
  222. include/seqan/consensus/overlap_info_computation.h
  223. include/seqan/consensus/overlapper.h
  224. include/seqan/file.h
  225. include/seqan/file/file_base.h
  226. include/seqan/file/file_cstyle.h
  227. include/seqan/file/file_forwards.h
  228. include/seqan/file/file_interface.h
  229. include/seqan/file/file_mapping.h
  230. include/seqan/file/file_page.h
  231. include/seqan/file/string_external.h
  232. include/seqan/file/string_mmap.h
  233. include/seqan/find.h
  234. include/seqan/find/find_abndm.h
  235. include/seqan/find/find_ahocorasick.h
  236. include/seqan/find/find_base.h
  237. include/seqan/find/find_begin.h
  238. include/seqan/find/find_bndm.h
  239. include/seqan/find/find_bom.h
  240. include/seqan/find/find_hamming_simple.h
  241. include/seqan/find/find_horspool.h
  242. include/seqan/find/find_lambda.h
  243. include/seqan/find/find_multi.h
  244. include/seqan/find/find_multiple_bfam.h
  245. include/seqan/find/find_multiple_shiftand.h
  246. include/seqan/find/find_myers_ukkonen.h
  247. include/seqan/find/find_pattern_base.h
  248. include/seqan/find/find_pex.h
  249. include/seqan/find/find_score.h
  250. include/seqan/find/find_set_horspool.h
  251. include/seqan/find/find_shiftand.h
  252. include/seqan/find/find_shiftor.h
  253. include/seqan/find/find_simple.h
  254. include/seqan/find/find_wild_shiftand.h
  255. include/seqan/find/find_wumanber.h
  256. include/seqan/gff_io.h
  257. include/seqan/gff_io/gff_file.h
  258. include/seqan/gff_io/gff_io_base.h
  259. include/seqan/graph_algorithms.h
  260. include/seqan/graph_algorithms/all_pairs_shortest_path.h
  261. include/seqan/graph_algorithms/bellman_ford.h
  262. include/seqan/graph_algorithms/bipartite_matching.h
  263. include/seqan/graph_algorithms/breadth_first_search.h
  264. include/seqan/graph_algorithms/connected_components.h
  265. include/seqan/graph_algorithms/depth_first_search.h
  266. include/seqan/graph_algorithms/dijkstra.h
  267. include/seqan/graph_algorithms/floyd_warshall.h
  268. include/seqan/graph_algorithms/ford_fulkerson.h
  269. include/seqan/graph_algorithms/graph_algorithm_heap_tree.h
  270. include/seqan/graph_algorithms/graph_algorithm_hmm.h
  271. include/seqan/graph_algorithms/graph_algorithm_lis_his.h
  272. include/seqan/graph_algorithms/kruskal.h
  273. include/seqan/graph_algorithms/path_growing.h
  274. include/seqan/graph_algorithms/prim.h
  275. include/seqan/graph_algorithms/single_source_shortest_path.h
  276. include/seqan/graph_algorithms/strongly_connected_compnents.h
  277. include/seqan/graph_algorithms/topological_sort.h
  278. include/seqan/graph_algorithms/transitive_closure.h
  279. include/seqan/graph_algorithms/weakly_connected_components.h
  280. include/seqan/graph_algorithms/weighted_bipartite_matching.h
  281. include/seqan/graph_align.h
  282. include/seqan/graph_align/graph_algorithm_refine_align.h
  283. include/seqan/graph_align/graph_algorithm_refine_aligngraph.h
  284. include/seqan/graph_align/graph_algorithm_refine_annotation.h
  285. include/seqan/graph_align/graph_algorithm_refine_exact.h
  286. include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h
  287. include/seqan/graph_align/graph_algorithm_refine_fragment.h
  288. include/seqan/graph_align/graph_algorithm_refine_inexact.h
  289. include/seqan/graph_align/graph_algorithm_refine_scoring.h
  290. include/seqan/graph_align/graph_impl_align.h
  291. include/seqan/graph_align/graph_impl_align_adapt.h
  292. include/seqan/graph_msa.h
  293. include/seqan/graph_msa/graph_align_tcoffee_base.h
  294. include/seqan/graph_msa/graph_align_tcoffee_distance.h
  295. include/seqan/graph_msa/graph_align_tcoffee_guidetree.h
  296. include/seqan/graph_msa/graph_align_tcoffee_io.h
  297. include/seqan/graph_msa/graph_align_tcoffee_kmer.h
  298. include/seqan/graph_msa/graph_align_tcoffee_library.h
  299. include/seqan/graph_msa/graph_align_tcoffee_msa.h
  300. include/seqan/graph_msa/graph_align_tcoffee_progressive.h
  301. include/seqan/graph_msa/graph_align_tcoffee_refinement.h
  302. include/seqan/graph_types.h
  303. include/seqan/graph_types/graph_base.h
  304. include/seqan/graph_types/graph_drawing.h
  305. include/seqan/graph_types/graph_edgestump.h
  306. include/seqan/graph_types/graph_idmanager.h
  307. include/seqan/graph_types/graph_impl_automaton.h
  308. include/seqan/graph_types/graph_impl_directed.h
  309. include/seqan/graph_types/graph_impl_hmm.h
  310. include/seqan/graph_types/graph_impl_oracle.h
  311. include/seqan/graph_types/graph_impl_tree.h
  312. include/seqan/graph_types/graph_impl_trie.h
  313. include/seqan/graph_types/graph_impl_undirected.h
  314. include/seqan/graph_types/graph_impl_wordgraph.h
  315. include/seqan/graph_types/graph_interface.h
  316. include/seqan/graph_types/graph_iterator.h
  317. include/seqan/graph_types/graph_iterator_adjacency.h
  318. include/seqan/graph_types/graph_iterator_bfs.h
  319. include/seqan/graph_types/graph_iterator_dfs.h
  320. include/seqan/graph_types/graph_iterator_edge.h
  321. include/seqan/graph_types/graph_iterator_outedge.h
  322. include/seqan/graph_types/graph_iterator_vertex.h
  323. include/seqan/graph_types/graph_utility_parsing.h
  324. include/seqan/graph_types/property_map_generic.h
  325. include/seqan/graph_types/property_map_internal.h
  326. include/seqan/graph_types/property_map_internal_pointer.h
  327. include/seqan/index.h
  328. include/seqan/index/find2_backtracking.h
  329. include/seqan/index/find2_base.h
  330. include/seqan/index/find2_functors.h
  331. include/seqan/index/find2_index.h
  332. include/seqan/index/find2_index_multi.h
  333. include/seqan/index/find2_vstree_factory.h
  334. include/seqan/index/find_backtracking.h
  335. include/seqan/index/find_index.h
  336. include/seqan/index/find_index_approx.h
  337. include/seqan/index/find_index_binary.h
  338. include/seqan/index/find_index_esa.h
  339. include/seqan/index/find_index_lambda.h
  340. include/seqan/index/find_index_qgram.h
  341. include/seqan/index/find_pigeonhole.h
  342. include/seqan/index/find_quasar.h
  343. include/seqan/index/find_swift.h
  344. include/seqan/index/index_base.h
  345. include/seqan/index/index_bidirectional.h
  346. include/seqan/index/index_bidirectional_stree.h
  347. include/seqan/index/index_bifm.h
  348. include/seqan/index/index_bifm_stree.h
  349. include/seqan/index/index_bwt.h
  350. include/seqan/index/index_childtab.h
  351. include/seqan/index/index_device.h
  352. include/seqan/index/index_dfi.h
  353. include/seqan/index/index_esa_algs.h
  354. include/seqan/index/index_esa_algs_multi.h
  355. include/seqan/index/index_esa_base.h
  356. include/seqan/index/index_esa_drawing.h
  357. include/seqan/index/index_esa_stree.h
  358. include/seqan/index/index_fm.h
  359. include/seqan/index/index_fm_compressed_sa.h
  360. include/seqan/index/index_fm_compressed_sa_iterator.h
  361. include/seqan/index/index_fm_dox.h
  362. include/seqan/index/index_fm_lf_table.h
  363. include/seqan/index/index_fm_rank_dictionary_base.h
  364. include/seqan/index/index_fm_rank_dictionary_levels.h
  365. include/seqan/index/index_fm_rank_dictionary_naive.h
  366. include/seqan/index/index_fm_rank_dictionary_wt.h
  367. include/seqan/index/index_fm_right_array_binary_tree.h
  368. include/seqan/index/index_fm_right_array_binary_tree_iterator.h
  369. include/seqan/index/index_fm_sparse_string.h
  370. include/seqan/index/index_fm_stree.h
  371. include/seqan/index/index_forwards.h
  372. include/seqan/index/index_lcp.h
  373. include/seqan/index/index_lcp_tree.h
  374. include/seqan/index/index_pizzachili.h
  375. include/seqan/index/index_pizzachili_find.h
  376. include/seqan/index/index_pizzachili_string.h
  377. include/seqan/index/index_qgram.h
  378. include/seqan/index/index_qgram_bucketrefinement.h
  379. include/seqan/index/index_qgram_openaddressing.h
  380. include/seqan/index/index_qgram_stree.h
  381. include/seqan/index/index_sa_btree.h
  382. include/seqan/index/index_sa_bwtwalk.h
  383. include/seqan/index/index_sa_lss.h
  384. include/seqan/index/index_sa_mm.h
  385. include/seqan/index/index_sa_qsort.h
  386. include/seqan/index/index_sa_stree.h
  387. include/seqan/index/index_sa_truncated.h
  388. include/seqan/index/index_shawarma.h
  389. include/seqan/index/index_shims.h
  390. include/seqan/index/index_skew3.h
  391. include/seqan/index/index_skew7.h
  392. include/seqan/index/index_skew7_multi.h
  393. include/seqan/index/index_view.h
  394. include/seqan/index/index_wotd.h
  395. include/seqan/index/pipe_merger3.h
  396. include/seqan/index/pipe_merger7.h
  397. include/seqan/index/pizzachili_api.h
  398. include/seqan/index/pump_extender3.h
  399. include/seqan/index/pump_extender7.h
  400. include/seqan/index/pump_lcp_core.h
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  1683. share/doc/seqan/html/page_DemoMaximalRepeats.html
  1684. share/doc/seqan/html/page_DemoMaximalUniqueMatches.html
  1685. share/doc/seqan/html/page_DemoMummy.html
  1686. share/doc/seqan/html/page_DemoSuffixArray.html
  1687. share/doc/seqan/html/page_DemoSupermaximalRepeats.html
  1688. share/doc/seqan/html/page_LanguageEntities.html
  1689. share/doc/seqan/html/page_mainpage.html
  1690. share/doc/seqan/html/specialization_AbndmAlgoPattern.html
  1691. share/doc/seqan/html/specialization_AdaptorIterator.html
  1692. share/doc/seqan/html/specialization_AdjacencyIterator.html
  1693. share/doc/seqan/html/specialization_AhoCorasickPattern.html
  1694. share/doc/seqan/html/specialization_AlignColIterator.html
  1695. share/doc/seqan/html/specialization_AlignmentGraph.html
  1696. share/doc/seqan/html/specialization_AllocString.html
  1697. share/doc/seqan/html/specialization_AminoAcid.html
  1698. share/doc/seqan/html/specialization_AnchorGaps.html
  1699. share/doc/seqan/html/specialization_AnnotationTreeIterator.html
  1700. share/doc/seqan/html/specialization_ArgParseOption.html
  1701. share/doc/seqan/html/specialization_ArrayGaps.html
  1702. share/doc/seqan/html/specialization_ArrayString.html
  1703. share/doc/seqan/html/specialization_AsyncFile.html
  1704. share/doc/seqan/html/specialization_AutoSeqFormat.html
  1705. share/doc/seqan/html/specialization_Automaton.html
  1706. share/doc/seqan/html/specialization_AverageAccumulator.html
  1707. share/doc/seqan/html/specialization_BadLexicalCast.html
  1708. share/doc/seqan/html/specialization_BaiBamIndex.html
  1709. share/doc/seqan/html/specialization_BamFileIn.html
  1710. share/doc/seqan/html/specialization_BamFileOut.html
  1711. share/doc/seqan/html/specialization_BandedLocalAlignmentEnumerator.html
  1712. share/doc/seqan/html/specialization_Bed12Record.html
  1713. share/doc/seqan/html/specialization_Bed3Record.html
  1714. share/doc/seqan/html/specialization_Bed4Record.html
  1715. share/doc/seqan/html/specialization_Bed5Record.html
  1716. share/doc/seqan/html/specialization_Bed6Record.html
  1717. share/doc/seqan/html/specialization_BedFileIn.html
  1718. share/doc/seqan/html/specialization_BedFileOut.html
  1719. share/doc/seqan/html/specialization_BfamPattern.html
  1720. share/doc/seqan/html/specialization_BfsIterator.html
  1721. share/doc/seqan/html/specialization_BitPackedPair.html
  1722. share/doc/seqan/html/specialization_BitPackedTuple.html
  1723. share/doc/seqan/html/specialization_BlastReportFileOut.html
  1724. share/doc/seqan/html/specialization_BlastTabularFileIn.html
  1725. share/doc/seqan/html/specialization_BlastTabularFileOut.html
  1726. share/doc/seqan/html/specialization_BlockString.html
  1727. share/doc/seqan/html/specialization_BndmAlgoPattern.html
  1728. share/doc/seqan/html/specialization_BottomUpIterator.html
  1729. share/doc/seqan/html/specialization_CStyleString.html
  1730. share/doc/seqan/html/specialization_Caster.html
  1731. share/doc/seqan/html/specialization_ChainedSeed.html
  1732. share/doc/seqan/html/specialization_ConcatDirectStringSet.html
  1733. share/doc/seqan/html/specialization_ConcatVirtualIterator.html
  1734. share/doc/seqan/html/specialization_ConcurrentSuspendableQueue.html
  1735. share/doc/seqan/html/specialization_Counter.html
  1736. share/doc/seqan/html/specialization_CountingIdManager.html
  1737. share/doc/seqan/html/specialization_D2AFScore.html
  1738. share/doc/seqan/html/specialization_D2StarAFScore.html
  1739. share/doc/seqan/html/specialization_D2zAFScore.html
  1740. share/doc/seqan/html/specialization_DPSearchPattern.html
  1741. share/doc/seqan/html/specialization_DeltaMapIterator.html
  1742. share/doc/seqan/html/specialization_DependentStringSet.html
  1743. share/doc/seqan/html/specialization_DfsPreorderIterator.html
  1744. share/doc/seqan/html/specialization_DirectedGraph.html
  1745. share/doc/seqan/html/specialization_Dna.html
  1746. share/doc/seqan/html/specialization_Dna5.html
  1747. share/doc/seqan/html/specialization_Dna5Q.html
  1748. share/doc/seqan/html/specialization_DnaQ.html
  1749. share/doc/seqan/html/specialization_Echoer.html
  1750. share/doc/seqan/html/specialization_EdgeIterator.html
  1751. share/doc/seqan/html/specialization_EditDistanceScore.html
  1752. share/doc/seqan/html/specialization_EditEnvironment.html
  1753. share/doc/seqan/html/specialization_EmptyFieldError.html
  1754. share/doc/seqan/html/specialization_Equidistant.html
  1755. share/doc/seqan/html/specialization_ExactFragment.html
  1756. share/doc/seqan/html/specialization_ExactReversableFragment.html
  1757. share/doc/seqan/html/specialization_ExternalString.html
  1758. share/doc/seqan/html/specialization_FMIndex.html
  1759. share/doc/seqan/html/specialization_Filter.html
  1760. share/doc/seqan/html/specialization_Finite.html
  1761. share/doc/seqan/html/specialization_FixedCyclicShape.html
  1762. share/doc/seqan/html/specialization_FormattedFileIn.html
  1763. share/doc/seqan/html/specialization_FormattedFileOut.html
  1764. share/doc/seqan/html/specialization_GappedShape.html
  1765. share/doc/seqan/html/specialization_GenericCyclicShape.html
  1766. share/doc/seqan/html/specialization_GenericShape.html
  1767. share/doc/seqan/html/specialization_GenerousDependentStringSet.html
  1768. share/doc/seqan/html/specialization_GffFileIn.html
  1769. share/doc/seqan/html/specialization_GffFileOut.html
  1770. share/doc/seqan/html/specialization_GlobalAlign.html
  1771. share/doc/seqan/html/specialization_GlobalChain.html
  1772. share/doc/seqan/html/specialization_HammingSimplePattern.html
  1773. share/doc/seqan/html/specialization_HammingStringEnumerator.html
  1774. share/doc/seqan/html/specialization_HardwiredShape.html
  1775. share/doc/seqan/html/specialization_HierarchicalPexPattern.html
  1776. share/doc/seqan/html/specialization_HmmGraph.html
  1777. share/doc/seqan/html/specialization_HorspoolPattern.html
  1778. share/doc/seqan/html/specialization_IndexDfi.html
  1779. share/doc/seqan/html/specialization_IndexEsa.html
  1780. share/doc/seqan/html/specialization_IndexQGram.html
  1781. share/doc/seqan/html/specialization_IndexSa.html
  1782. share/doc/seqan/html/specialization_IndexWotd.html
  1783. share/doc/seqan/html/specialization_InfixSegment.html
  1784. share/doc/seqan/html/specialization_InputStreamIterator.html
  1785. share/doc/seqan/html/specialization_IteratorProxy.html
  1786. share/doc/seqan/html/specialization_Iupac.html
  1787. share/doc/seqan/html/specialization_Joiner.html
  1788. share/doc/seqan/html/specialization_JournaledSet.html
  1789. share/doc/seqan/html/specialization_JournaledString.html
  1790. share/doc/seqan/html/specialization_LevenshteinStringEnumerator.html
  1791. share/doc/seqan/html/specialization_MMapString.html
  1792. share/doc/seqan/html/specialization_MapperConfig.html
  1793. share/doc/seqan/html/specialization_MapperConfigSize.html
  1794. share/doc/seqan/html/specialization_MapperSpec.html
  1795. share/doc/seqan/html/specialization_MatrixScore.html
  1796. share/doc/seqan/html/specialization_MaxRepeatsIterator.html
  1797. share/doc/seqan/html/specialization_ModCyclicShapeModifiedIterator.html
  1798. share/doc/seqan/html/specialization_ModCyclicShapeModifiedString.html
  1799. share/doc/seqan/html/specialization_ModPaddingIterator.html
  1800. share/doc/seqan/html/specialization_ModPaddingString.html
  1801. share/doc/seqan/html/specialization_ModReverseIterator.html
  1802. share/doc/seqan/html/specialization_ModReverseString.html
  1803. share/doc/seqan/html/specialization_ModViewModifiedIterator.html
  1804. share/doc/seqan/html/specialization_ModViewModifiedString.html
  1805. share/doc/seqan/html/specialization_MultiBfamPattern.html
  1806. share/doc/seqan/html/specialization_MultiMemsIterator.html
  1807. share/doc/seqan/html/specialization_MultiPoolAllocator.html
  1808. share/doc/seqan/html/specialization_MultipleShiftAndPattern.html
  1809. share/doc/seqan/html/specialization_MumsIterator.html
  1810. share/doc/seqan/html/specialization_MyersPattern.html
  1811. share/doc/seqan/html/specialization_N2AFScore.html
  1812. share/doc/seqan/html/specialization_Namer.html
  1813. share/doc/seqan/html/specialization_NonHierarchicalPexPattern.html
  1814. share/doc/seqan/html/specialization_OneGappedShape.html
  1815. share/doc/seqan/html/specialization_OpenAddressingQGramIndex.html
  1816. share/doc/seqan/html/specialization_OracleBfamPattern.html
  1817. share/doc/seqan/html/specialization_OracleMultiBfamPattern.html
  1818. share/doc/seqan/html/specialization_OutEdgeIterator.html
  1819. share/doc/seqan/html/specialization_OutputStreamIterator.html
  1820. share/doc/seqan/html/specialization_OwnerStringSet.html
  1821. share/doc/seqan/html/specialization_PackedPair.html
  1822. share/doc/seqan/html/specialization_PackedString.html
  1823. share/doc/seqan/html/specialization_PackedTriple.html
  1824. share/doc/seqan/html/specialization_ParseError.html
  1825. share/doc/seqan/html/specialization_PexPattern.html
  1826. share/doc/seqan/html/specialization_PigeonholeFinder.html
  1827. share/doc/seqan/html/specialization_PigeonholePattern.html
  1828. share/doc/seqan/html/specialization_PizzaChiliIndex.html
  1829. share/doc/seqan/html/specialization_PizzaChiliString.html
  1830. share/doc/seqan/html/specialization_PoolConfig.html
  1831. share/doc/seqan/html/specialization_PoolConfigSize.html
  1832. share/doc/seqan/html/specialization_PoolSpec.html
  1833. share/doc/seqan/html/specialization_PositionIterator.html
  1834. share/doc/seqan/html/specialization_PrefixSegment.html
  1835. share/doc/seqan/html/specialization_PriorityHeap.html
  1836. share/doc/seqan/html/specialization_ProfileSeqFracScore.html
  1837. share/doc/seqan/html/specialization_ProfileSeqScore.html
  1838. share/doc/seqan/html/specialization_ReducedAminoAcid.html
  1839. share/doc/seqan/html/specialization_ResizableContainerView.html
  1840. share/doc/seqan/html/specialization_RightArrayBinaryTreeIterator.html
  1841. share/doc/seqan/html/specialization_Rna.html
  1842. share/doc/seqan/html/specialization_Rna5.html
  1843. share/doc/seqan/html/specialization_RoiFileIn.html
  1844. share/doc/seqan/html/specialization_RoiFileOut.html
  1845. share/doc/seqan/html/specialization_Sampler.html
  1846. share/doc/seqan/html/specialization_ScoreSimdWrapper.html
  1847. share/doc/seqan/html/specialization_SeqFileIn.html
  1848. share/doc/seqan/html/specialization_SeqFileOut.html
  1849. share/doc/seqan/html/specialization_SetHorspoolPattern.html
  1850. share/doc/seqan/html/specialization_ShiftAndPattern.html
  1851. share/doc/seqan/html/specialization_ShiftOrPattern.html
  1852. share/doc/seqan/html/specialization_Shifter.html
  1853. share/doc/seqan/html/specialization_SimpleAllocator.html
  1854. share/doc/seqan/html/specialization_SimpleHolder.html
  1855. share/doc/seqan/html/specialization_SimpleIntervalsFileIn.html
  1856. share/doc/seqan/html/specialization_SimpleIntervalsFileInOut.html
  1857. share/doc/seqan/html/specialization_SimplePattern.html
  1858. share/doc/seqan/html/specialization_SimpleScore.html
  1859. share/doc/seqan/html/specialization_SimpleSeed.html
  1860. share/doc/seqan/html/specialization_SimpleShape.html
  1861. share/doc/seqan/html/specialization_SinglePoolAllocator.html
  1862. share/doc/seqan/html/specialization_Skiplist.html
  1863. share/doc/seqan/html/specialization_SorterConfig.html
  1864. share/doc/seqan/html/specialization_SorterConfigSize.html
  1865. share/doc/seqan/html/specialization_SorterSpec.html
  1866. share/doc/seqan/html/specialization_Source.html
  1867. share/doc/seqan/html/specialization_StdAdaptorIterator.html
  1868. share/doc/seqan/html/specialization_StoreIntervalsIntervalTreeNode.html
  1869. share/doc/seqan/html/specialization_StorePointsOnlyIntervalTreeNode.html
  1870. share/doc/seqan/html/specialization_StreamIterator.html
  1871. share/doc/seqan/html/specialization_SuffixSegment.html
  1872. share/doc/seqan/html/specialization_SuperMaxRepeatsFastIterator.html
  1873. share/doc/seqan/html/specialization_SuperMaxRepeatsIterator.html
  1874. share/doc/seqan/html/specialization_SwiftFinder.html
  1875. share/doc/seqan/html/specialization_SwiftLocalFinder.html
  1876. share/doc/seqan/html/specialization_SwiftLocalPattern.html
  1877. share/doc/seqan/html/specialization_SwiftPattern.html
  1878. share/doc/seqan/html/specialization_SwiftSemiGlobalFinder.html
  1879. share/doc/seqan/html/specialization_SwiftSemiGlobalPattern.html
  1880. share/doc/seqan/html/specialization_SyncFile.html
  1881. share/doc/seqan/html/specialization_TightDependentStringSet.html
  1882. share/doc/seqan/html/specialization_TopDownHistoryIterator.html
  1883. share/doc/seqan/html/specialization_TopDownIterator.html
  1884. share/doc/seqan/html/specialization_Tree.html
  1885. share/doc/seqan/html/specialization_TrieBfamPattern.html
  1886. share/doc/seqan/html/specialization_TristateHolder.html
  1887. share/doc/seqan/html/specialization_Tupler.html
  1888. share/doc/seqan/html/specialization_TwoLevelRankDictionary.html
  1889. share/doc/seqan/html/specialization_UcscFileIn.html
  1890. share/doc/seqan/html/specialization_UcscFileOut.html
  1891. share/doc/seqan/html/specialization_UnbandedLocalAlignmentEnumerator.html
  1892. share/doc/seqan/html/specialization_UndirectedGraph.html
  1893. share/doc/seqan/html/specialization_UnexpectedEnd.html
  1894. share/doc/seqan/html/specialization_UngappedShape.html
  1895. share/doc/seqan/html/specialization_VSTreeIterator.html
  1896. share/doc/seqan/html/specialization_VcfFileIn.html
  1897. share/doc/seqan/html/specialization_VcfFileOut.html
  1898. share/doc/seqan/html/specialization_VectorSet.html
  1899. share/doc/seqan/html/specialization_VertexIterator.html
  1900. share/doc/seqan/html/specialization_WaveletTree.html
  1901. share/doc/seqan/html/specialization_WildShiftAndPattern.html
  1902. share/doc/seqan/html/specialization_WordGraph.html
  1903. share/doc/seqan/html/specialization_WuManberPattern.html
  1904. share/doc/seqan/html/specialization_ZipContainerView.html
  1905. share/doc/seqan/html/specialization_ZipIterator.html
  1906. share/doc/seqan/html/tag_Default.html
  1907. share/doc/seqan/html/tag_DotDrawing.html
  1908. share/doc/seqan/html/tag_EditDistance.html
  1909. share/doc/seqan/html/tag_GeneticCode.html
  1910. share/doc/seqan/html/tag_HammingDistance.html
  1911. share/doc/seqan/html/tag_LevenshteinDistance.html
  1912. share/doc/seqan/html/tag_Move.html
  1913. share/doc/seqan/html/tag_Murphy10.html
  1914. share/doc/seqan/html/tag_Nothing.html
  1915. share/doc/seqan/html/variable_BAM_95FLAG_95SUPPLEMENTARY_32_61_320x0800.html
  1916. share/doc/seqan/html/variable_LibraryStoreElementstd.html
  1917. Collapse this list.

To install the port: cd /usr/ports/biology/seqan/ && make install clean
To add the package: pkg install seqan

PKGNAME: seqan

distinfo:

TIMESTAMP = 1473846790
SHA256 (seqan-library-2.2.0.tar.xz) = b5c036a3d2fc2fe5f2d57dcd4d7c523a6df146ab7b44bc789f42004b058d72fd
SIZE (seqan-library-2.2.0.tar.xz) = 5223004

There are no ports dependent upon this port


Configuration Options
===> The following configuration options are available for seqan-2.2.0:
     DOCS=on: Install official API documentation (html)
===> Use 'make config' to modify these settings

USES:
tar:xz

Master Sites:
  1. http://packages.seqan.de/seqan-library/
Notes from UPDATING
These upgrade notes are taken from /usr/ports/UPDATING
  • 2016-05-10
    Affects: users of biology/seqan
    Author: junovitch@FreeBSD.org
    Reason: 
      The biology/seqan port has been split into biology/seqan (only the
      library) and biology/seqan-apps for the programs based on SeqAn. Both
      ports are based on version 2.1.1 of the SeqAn repository. There is a new
      biology/seqan1 port with version 1.3 of SeqAn for backwards compatibility,
      but this port will likely be deprecated in the next year so please update
      your software to SeqAn2.
    
    

Number of commits found: 18

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
14 Sep 2016 19:38:58
Original commit files touched by this commit  2.2.0
Revision:422156
pawel search for other commits by this committer
- Update biology/seqan and bilogy/seqan-apps to version 2.2.0 [1]
- Fix spelling in pkg-descr

PR:		212682 [1]
Submitted by:	Hannes Hauswedell (maintainer) [1]
27 May 2016 16:10:36
Original commit files touched by this commit  2.1.1_1
Revision:415945
amdmi3 search for other commits by this committer
- Do install cmake and pkgconfig modules
- While here, switch to options helpers

PR:		209710
Submitted by:	h2+fbsdports@fsfe.org (maintainer)
10 May 2016 01:05:23
Original commit files touched by this commit  2.1.1
Revision:414898
junovitch search for other commits by this committer
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>
21 Mar 2015 11:53:28
Original commit files touched by this commit  1.3.1_3
Revision:381791
marino search for other commits by this committer
biology/segan: Limit GCC to 4.8 while waiting for update

Due to questionable c++, GCC 4.9 and newer cannot build seqan.  An update
has been in the works that will enable clang compilers and all versions
of GCC to build seqan, but it is not quite ready yet.  While waiting for
it, limit the version of GCC used to 4.8.

PR:	196851
20 Oct 2014 07:10:48
Original commit files touched by this commit  1.3.1_3
Revision:371237
bapt search for other commits by this committer
Cleanup plist
19 Oct 2014 07:38:12
Original commit files touched by this commit  1.3.1_3
Revision:371171
mva search for other commits by this committer
- Convert ports from benchmarks/ and biology/ to new USES=python

Approved by:	portmgr (implicit)
10 Sep 2014 20:50:37
Original commit files touched by this commit  1.3.1_3
Revision:367888
gerald search for other commits by this committer
Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)
10 Jul 2014 22:29:52
Original commit files touched by this commit  1.3.1_2
Revision:361497
adamw search for other commits by this committer
Use gcc on all platforms.

PR:		191692
Submitted by:	maintainer
01 Jun 2014 11:42:17
Original commit files touched by this commit  1.3.1_2
Revision:356100
ohauer search for other commits by this committer
- add stage support
- adjust BSDn license
10 Mar 2014 20:55:22
Original commit files touched by this commit  1.3.1_2
Revision:347809
gerald search for other commits by this committer
Update the default version of GCC used in the Ports Collection from
GCC 4.6.4 to GCC 4.7.3.  This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.

Part II, Bump PORTREVISIONs.

PR:		182136
Supported by:	Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by:	bdrewery (two -exp runs)
07 Mar 2014 15:52:40
Original commit files touched by this commit  1.3.1_1
Revision:347402
bapt search for other commits by this committer
Convert b* to USES=zip
26 Oct 2013 00:52:36
Original commit files touched by this commit  1.3.1_1
Revision:331644
gerald search for other commits by this committer
Update to libmpc version 1.0.1 which brings the following fixes:

 - Switched to automake 1.11.6, see CVE-2012-3386.
 - #14669: Fixed extraction of CC from gmp.h.
 - Fixed case of intermediate zero real or imaginary part in mpc_fma,
   found by hydra with GMP_CHECK_RANDOMIZE=1346362345.

This is on top of the following changes from version 1.0

 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
   invariant sections) for the documentation.
 - 100% of all lines are covered by tests
 - Renamed functions
   . mpc_mul_2exp to mpc_mul_2ui
   . mpc_div_2exp to mpc_div_2ui
(Only the first 15 lines of the commit message are shown above View all of this commit message)
20 Sep 2013 15:55:44
Original commit files touched by this commit  1.3.1
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
17 Aug 2013 16:27:24
Original commit files touched by this commit  1.3.1
Revision:324851
gerald search for other commits by this committer
Replace USE_GCC=4.6+ and USE_GCC=4.4+ by USE_GCC=yes.

Right now this is a noop in the former case and a noop in the latter
case unless lang/gcc44 has been installed explicitly.

This puts a bit more emphasis on standardizing on a canonical version
"current" GCC and makes it easier to update that canonical version
by changing the default in Mk/bsd.gcc.mk and updating the lang/gcc port.

That is, USE_GCC=yes means "use a decent/modern version of GCC" without
having to worry about details.

Approved by:	portmgr (bdrewery)
22 Mar 2013 20:06:15
Original commit files touched by this commit  1.3.1
Revision:314960
makc search for other commits by this committer
- convert USE_CMAKE to USES
- while here clean up some ports from CMAKE_VERBOSE, which is intended
  for users

Approved by:	portmgr (miwi)
21 Jul 2012 22:20:33
Original commit files touched by this commit  1.3.1
gerald search for other commits by this committer
Replace USE_GCC=4.4+ by USE_GCC=4.6+ since GCC 4.4 is on its way out.

Approved by:	maintainer
07 Jun 2012 13:04:53
Original commit files touched by this commit  1.3.1
amdmi3 search for other commits by this committer
- Fix maintainer email

Submitted by:   maintainer via private email
06 Jun 2012 17:51:33
Original commit files touched by this commit  1.3.1
amdmi3 search for other commits by this committer
SeqAn is an open source C++ library of efficient algorithms
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.

WWW: http://www.seqan.de/

PR:             167571
Submitted by:   Hannes <h2+fbsdports@fsfe.org>

Number of commits found: 18

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openssl-develNov 02
wordpressNov 01
php56Oct 30
php70Oct 30
php71Oct 30
wiresharkOct 30
chromiumOct 28
wgetOct 27
wgetOct 27
openoffice-4*Oct 26
openoffice-devel*Oct 26
gitlabOct 25
nodeOct 25
node4Oct 25

No vulnerabilities have been reported in the past 14 days

* - modified, not new

All vulnerabilities


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Calculated hourly:
Port count 31894
Broken 125
Deprecated 46
Ignore 361
Forbidden 0
Restricted 173
No CDROM 78
Vulnerable 48
Expired 11
Set to expire 38
Interactive 0
new 24 hours 3
new 48 hours15
new 7 days127
new fortnight3283
new month3481

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