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Port details
ugene Integrated bioinformatics toolkit
40.1 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 View this port on Repology. pkg-fallout 40.0Version of this port present on the latest quarterly branch.
Maintainer: h2+fbsdports@fsfe.org search for ports maintained by this maintainer
Port Added: 2013-02-23 04:51:12
Last Update: 2021-10-14 11:23:37
Commit Hash: e409be3
Also Listed In: science
License: GPLv2+
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (1326 items)
Collapse this list.
  1. @desktop-file-utils
  2. @shared-mime-info share/mime
  3. /usr/local/share/licenses/ugene-40.1/catalog.mk
  4. /usr/local/share/licenses/ugene-40.1/LICENSE
  5. /usr/local/share/licenses/ugene-40.1/GPLv2+
  6. bin/ugene
  7. lib/ugene/libQSpec.so
  8. lib/ugene/libU2Algorithm.so
  9. lib/ugene/libU2Core.so
  10. lib/ugene/libU2Designer.so
  11. lib/ugene/libU2Formats.so
  12. lib/ugene/libU2Gui.so
  13. lib/ugene/libU2Lang.so
  14. lib/ugene/libU2Private.so
  15. lib/ugene/libU2Script.so
  16. lib/ugene/libU2Test.so
  17. lib/ugene/libU2View.so
  18. lib/ugene/plugins/CoreTests.license
  19. lib/ugene/plugins/CoreTests.plugin
  20. lib/ugene/plugins/GUITestBase.license
  21. lib/ugene/plugins/GUITestBase.plugin
  22. lib/ugene/plugins/annotator.license
  23. lib/ugene/plugins/annotator.plugin
  24. lib/ugene/plugins/api_tests.license
  25. lib/ugene/plugins/api_tests.plugin
  26. lib/ugene/plugins/ball.license
  27. lib/ugene/plugins/ball.plugin
  28. lib/ugene/plugins/biostruct3d_view.license
  29. lib/ugene/plugins/biostruct3d_view.plugin
  30. lib/ugene/plugins/chroma_view.license
  31. lib/ugene/plugins/chroma_view.plugin
  32. lib/ugene/plugins/circular_view.license
  33. lib/ugene/plugins/circular_view.plugin
  34. lib/ugene/plugins/clark_support.license
  35. lib/ugene/plugins/clark_support.plugin
  36. lib/ugene/plugins/dbi_bam.license
  37. lib/ugene/plugins/dbi_bam.plugin
  38. lib/ugene/plugins/diamond_support.license
  39. lib/ugene/plugins/diamond_support.plugin
  40. lib/ugene/plugins/dna_export.license
  41. lib/ugene/plugins/dna_export.plugin
  42. lib/ugene/plugins/dna_flexibility.license
  43. lib/ugene/plugins/dna_flexibility.plugin
  44. lib/ugene/plugins/dna_graphpack.license
  45. lib/ugene/plugins/dna_graphpack.plugin
  46. lib/ugene/plugins/dna_stat.license
  47. lib/ugene/plugins/dna_stat.plugin
  48. lib/ugene/plugins/dotplot.license
  49. lib/ugene/plugins/dotplot.plugin
  50. lib/ugene/plugins/enzymes.license
  51. lib/ugene/plugins/enzymes.plugin
  52. lib/ugene/plugins/external_tool_support.license
  53. lib/ugene/plugins/external_tool_support.plugin
  54. lib/ugene/plugins/genome_aligner.license
  55. lib/ugene/plugins/genome_aligner.plugin
  56. lib/ugene/plugins/gor4.license
  57. lib/ugene/plugins/gor4.plugin
  58. lib/ugene/plugins/hmm2.license
  59. lib/ugene/plugins/hmm2.plugin
  60. lib/ugene/plugins/kalign.license
  61. lib/ugene/plugins/kalign.plugin
  62. lib/ugene/plugins/kraken_support.license
  63. lib/ugene/plugins/kraken_support.plugin
  64. lib/ugene/plugins/libCoreTests.so
  65. lib/ugene/plugins/libGUITestBase.so
  66. lib/ugene/plugins/libannotator.so
  67. lib/ugene/plugins/libapi_tests.so
  68. lib/ugene/plugins/libball.so
  69. lib/ugene/plugins/libbiostruct3d_view.so
  70. lib/ugene/plugins/libchroma_view.so
  71. lib/ugene/plugins/libcircular_view.so
  72. lib/ugene/plugins/libclark_support.so
  73. lib/ugene/plugins/libdbi_bam.so
  74. lib/ugene/plugins/libdiamond_support.so
  75. lib/ugene/plugins/libdna_export.so
  76. lib/ugene/plugins/libdna_flexibility.so
  77. lib/ugene/plugins/libdna_graphpack.so
  78. lib/ugene/plugins/libdna_stat.so
  79. lib/ugene/plugins/libdotplot.so
  80. lib/ugene/plugins/libenzymes.so
  81. lib/ugene/plugins/libexternal_tool_support.so
  82. lib/ugene/plugins/libgenome_aligner.so
  83. lib/ugene/plugins/libgor4.so
  84. lib/ugene/plugins/libhmm2.so
  85. lib/ugene/plugins/libkalign.so
  86. lib/ugene/plugins/libkraken_support.so
  87. lib/ugene/plugins/liblinkdata_support.so
  88. lib/ugene/plugins/libmetaphlan2_support.so
  89. lib/ugene/plugins/libngs_reads_classification.so
  90. lib/ugene/plugins/libopencl_support.so
  91. lib/ugene/plugins/liborf_marker.so
  92. lib/ugene/plugins/libpcr.so
  93. lib/ugene/plugins/libperf_monitor.so
  94. lib/ugene/plugins/libphylip.so
  95. lib/ugene/plugins/libprimer3.so
  96. lib/ugene/plugins/libpsipred.so
  97. lib/ugene/plugins/libptools.so
  98. lib/ugene/plugins/libquery_designer.so
  99. lib/ugene/plugins/libremote_blast.so
  100. lib/ugene/plugins/librepeat_finder.so
  101. lib/ugene/plugins/libsitecon.so
  102. lib/ugene/plugins/libsmith_waterman.so
  103. lib/ugene/plugins/libtest_runner.so
  104. lib/ugene/plugins/libumuscle.so
  105. lib/ugene/plugins/libvariants.so
  106. lib/ugene/plugins/libweight_matrix.so
  107. lib/ugene/plugins/libwevote_support.so
  108. lib/ugene/plugins/libworkflow_designer.so
  109. lib/ugene/plugins/linkdata_support.license
  110. lib/ugene/plugins/linkdata_support.plugin
  111. lib/ugene/plugins/metaphlan2_support.license
  112. lib/ugene/plugins/metaphlan2_support.plugin
  113. lib/ugene/plugins/ngs_reads_classification.license
  114. lib/ugene/plugins/ngs_reads_classification.plugin
  115. lib/ugene/plugins/opencl_support.license
  116. lib/ugene/plugins/opencl_support.plugin
  117. lib/ugene/plugins/orf_marker.license
  118. lib/ugene/plugins/orf_marker.plugin
  119. lib/ugene/plugins/pcr.license
  120. lib/ugene/plugins/pcr.plugin
  121. lib/ugene/plugins/perf_monitor.license
  122. lib/ugene/plugins/perf_monitor.plugin
  123. lib/ugene/plugins/phylip.license
  124. lib/ugene/plugins/phylip.plugin
  125. lib/ugene/plugins/primer3.license
  126. lib/ugene/plugins/primer3.plugin
  127. lib/ugene/plugins/psipred.license
  128. lib/ugene/plugins/psipred.plugin
  129. lib/ugene/plugins/ptools.license
  130. lib/ugene/plugins/ptools.plugin
  131. lib/ugene/plugins/query_designer.license
  132. lib/ugene/plugins/query_designer.plugin
  133. lib/ugene/plugins/remote_blast.license
  134. lib/ugene/plugins/remote_blast.plugin
  135. lib/ugene/plugins/repeat_finder.license
  136. lib/ugene/plugins/repeat_finder.plugin
  137. lib/ugene/plugins/sitecon.license
  138. lib/ugene/plugins/sitecon.plugin
  139. lib/ugene/plugins/smith_waterman.license
  140. lib/ugene/plugins/smith_waterman.plugin
  141. lib/ugene/plugins/test_runner.license
  142. lib/ugene/plugins/test_runner.plugin
  143. lib/ugene/plugins/umuscle.license
  144. lib/ugene/plugins/umuscle.plugin
  145. lib/ugene/plugins/variants.license
  146. lib/ugene/plugins/variants.plugin
  147. lib/ugene/plugins/weight_matrix.license
  148. lib/ugene/plugins/weight_matrix.plugin
  149. lib/ugene/plugins/wevote_support.license
  150. lib/ugene/plugins/wevote_support.plugin
  151. lib/ugene/plugins/workflow_designer.license
  152. lib/ugene/plugins/workflow_designer.plugin
  153. lib/ugene/plugins_checker
  154. lib/ugene/transl_ru.qm
  155. lib/ugene/transl_tr.qm
  156. lib/ugene/ugene
  157. lib/ugene/ugenecl
  158. lib/ugene/ugenem
  159. lib/ugene/ugeneui
  160. man/man1/ugene.1.gz
  161. share/applications/ugene.desktop
  162. share/icons/hicolor/32x32/mimetypes/application-x-ugene-ext.png
  163. share/mime/packages/application-x-ugene.xml
  164. share/pixmaps/ugene.png
  165. share/pixmaps/ugene.xpm
  166. share/ugene/DBXRefRegistry.txt
  167. share/ugene/adapters/adapters.fasta
  168. share/ugene/adapters/illumina/NexteraPE-PE.fa
  169. share/ugene/adapters/illumina/TruSeq2-PE.fa
  170. share/ugene/adapters/illumina/TruSeq2-SE.fa
  171. share/ugene/adapters/illumina/TruSeq3-PE-2.fa
  172. share/ugene/adapters/illumina/TruSeq3-PE.fa
  173. share/ugene/adapters/illumina/TruSeq3-SE.fa
  174. share/ugene/back_translation/Bacteria/Arthrobacter_aurescens_TC1.cut
  175. share/ugene/back_translation/Bacteria/Bacillus_subtilis.cut
  176. share/ugene/back_translation/Bacteria/Escherichia_coli.cut
  177. share/ugene/back_translation/Bacteria/Haemophilus_influenzae.cut
  178. share/ugene/back_translation/Bacteria/Helicobacter_pylori.cut
  179. share/ugene/back_translation/Bacteria/Listeria_monocytogenes.cut
  180. share/ugene/back_translation/Bacteria/Neisseria_meningitidis.cut
  181. share/ugene/back_translation/Bacteria/Salmonella_typhimurium_LT2.cut
  182. share/ugene/back_translation/Bacteria/Streptomyces_coelicolor_A3(2).cut
  183. share/ugene/back_translation/Bacteria/Sulfolobus_solfataricus_P2.cut
  184. share/ugene/back_translation/Invertebrates/Apis_mellifera_(honey_bee).cut
  185. share/ugene/back_translation/Invertebrates/Caenorhabditis_elegans.cut
  186. share/ugene/back_translation/Invertebrates/Drosophila_melanogaster_(fruit_fly).cut
  187. share/ugene/back_translation/Invertebrates/Plasmodium_falciparum_(malaria_parasite_P._falciparum).cut
  188. share/ugene/back_translation/Invertebrates/mitochondrion_Caenorhabditis_elegans.cut
  189. share/ugene/back_translation/Invertebrates/mitochondrion_Drosophila_melanogaster_(fruit_fly).cut
  190. share/ugene/back_translation/Mammalia/Bos_taurus_(cow).cut
  191. share/ugene/back_translation/Mammalia/Canis_familiaris_(dog).cut
  192. share/ugene/back_translation/Mammalia/Sus_scrofa_(pig).cut
  193. share/ugene/back_translation/Mammalia/mitochondrion_Bos_taurus_(cow).cut
  194. share/ugene/back_translation/Mammalia/mitochondrion_Sus_scrofa_(pig).cut
  195. share/ugene/back_translation/Plants/Arabidopsis_thaliana_(thale_cress).cut
  196. share/ugene/back_translation/Plants/Oryza_sativa.cut
  197. share/ugene/back_translation/Plants/Zea_mays.cut
  198. share/ugene/back_translation/Primates/Homo_sapiens_(human).cut
  199. share/ugene/back_translation/Primates/Pan_troglodytes_(chimpanzee).cut
  200. share/ugene/back_translation/Primates/mitochondrion_Homo_sapiens_(human).cut
  201. share/ugene/back_translation/Primates/mitochondrion_Pan_troglodytes_(chimpanzee).cut
  202. share/ugene/back_translation/Rodents/Mus_musculus_(house_mouse).cut
  203. share/ugene/back_translation/Rodents/Rattus_norvegicus_(Norway_rat).cut
  204. share/ugene/back_translation/Vertebrates/Gallus_gallus_(chicken).cut
  205. share/ugene/back_translation/Vertebrates/Takifugu_rubripes_(Fugu_rubripes).cut
  206. share/ugene/back_translation/Vertebrates/Xenopus_laevis_(African_clawed_frog).cut
  207. share/ugene/back_translation/Vertebrates/mitochondrion_Gallus_gallus_(chicken).cut
  208. share/ugene/back_translation/Vertebrates/mitochondrion_Takifugu_rubripes_(Fugu_rubripes).cut
  209. share/ugene/back_translation/Viruses/Human_immunodeficiency_virus_1_(HIV-1).cut
  210. share/ugene/back_translation/Viruses/Influenza_A_virus.cut
  211. share/ugene/back_translation/Yeast/Saccharomyces_cerevisiae_(baker's_yeast).cut
  212. share/ugene/back_translation/tables.xml
  213. share/ugene/biostruct3d_plugin/BioStruct3DLinks.txt
  214. share/ugene/cmdline/align-clustalo.uwl
  215. share/ugene/cmdline/align-clustalw.uwl
  216. share/ugene/cmdline/align-kalign.uwl
  217. share/ugene/cmdline/align-mafft.uwl
  218. share/ugene/cmdline/align-tcoffee.uwl
  219. share/ugene/cmdline/align-to-reference.uwl
  220. share/ugene/cmdline/align.uwl
  221. share/ugene/cmdline/convert-msa.uwl
  222. share/ugene/cmdline/convert-seq.uwl
  223. share/ugene/cmdline/extract-sequence.uwl
  224. share/ugene/cmdline/extract_consensus_sequence.uwl
  225. share/ugene/cmdline/extract_consensus_string.uwl
  226. share/ugene/cmdline/extract_coverage.uwl
  227. share/ugene/cmdline/fetch-sequence.uwl
  228. share/ugene/cmdline/find-orfs.uwl
  229. share/ugene/cmdline/find-repeats.uwl
  230. share/ugene/cmdline/find-sw.uwl
  231. share/ugene/cmdline/gene-by-gene.uwl
  232. share/ugene/cmdline/generate-dna.uwl
  233. share/ugene/cmdline/hmm2-build.uwl
  234. share/ugene/cmdline/hmm2-search.uwl
  235. share/ugene/cmdline/hmm3-build-and-search.uwl
  236. share/ugene/cmdline/hmm3-search.uwl
  237. share/ugene/cmdline/join-quality.uwl
  238. share/ugene/cmdline/local-blast+.uwl
  239. share/ugene/cmdline/pfm-build.uwl
  240. share/ugene/cmdline/pfm-search.uwl
  241. share/ugene/cmdline/pwm-build.uwl
  242. share/ugene/cmdline/pwm-search.uwl
  243. share/ugene/cmdline/query.uwl
  244. share/ugene/cmdline/remote-request.uwl
  245. share/ugene/cmdline/revcompl.uwl
  246. share/ugene/cmdline/sitecon-build.uwl
  247. share/ugene/cmdline/sitecon-search.uwl
  248. share/ugene/cmdline/snp.uwl
  249. share/ugene/custom_annotations/plasmid_features.txt
  250. share/ugene/enzymes/2013_08_01.bairoch.gz
  251. share/ugene/genome_lengths/danRer7.genome
  252. share/ugene/genome_lengths/ecoli.genome
  253. share/ugene/genome_lengths/hg18.genome
  254. share/ugene/genome_lengths/hg19.genome
  255. share/ugene/genome_lengths/mm10.genome
  256. share/ugene/genome_lengths/mm8.genome
  257. share/ugene/genome_lengths/mm9.genome
  258. share/ugene/genome_lengths/test.genome
  259. share/ugene/license
  260. share/ugene/position_weight_matrix/JASPAR/all_jaspar.csv
  261. share/ugene/position_weight_matrix/JASPAR/fungi/MA0265.1.pfm
  262. share/ugene/position_weight_matrix/JASPAR/fungi/MA0266.1.pfm
  263. share/ugene/position_weight_matrix/JASPAR/fungi/MA0267.1.pfm
  264. share/ugene/position_weight_matrix/JASPAR/fungi/MA0268.1.pfm
  265. share/ugene/position_weight_matrix/JASPAR/fungi/MA0269.1.pfm
  266. share/ugene/position_weight_matrix/JASPAR/fungi/MA0270.1.pfm
  267. share/ugene/position_weight_matrix/JASPAR/fungi/MA0271.1.pfm
  268. share/ugene/position_weight_matrix/JASPAR/fungi/MA0272.1.pfm
  269. share/ugene/position_weight_matrix/JASPAR/fungi/MA0273.1.pfm
  270. share/ugene/position_weight_matrix/JASPAR/fungi/MA0274.1.pfm
  271. share/ugene/position_weight_matrix/JASPAR/fungi/MA0275.1.pfm
  272. share/ugene/position_weight_matrix/JASPAR/fungi/MA0276.1.pfm
  273. share/ugene/position_weight_matrix/JASPAR/fungi/MA0277.1.pfm
  274. share/ugene/position_weight_matrix/JASPAR/fungi/MA0278.1.pfm
  275. share/ugene/position_weight_matrix/JASPAR/fungi/MA0279.1.pfm
  276. share/ugene/position_weight_matrix/JASPAR/fungi/MA0280.1.pfm
  277. share/ugene/position_weight_matrix/JASPAR/fungi/MA0281.1.pfm
  278. share/ugene/position_weight_matrix/JASPAR/fungi/MA0282.1.pfm
  279. share/ugene/position_weight_matrix/JASPAR/fungi/MA0283.1.pfm
  280. share/ugene/position_weight_matrix/JASPAR/fungi/MA0284.1.pfm
  281. share/ugene/position_weight_matrix/JASPAR/fungi/MA0285.1.pfm
  282. share/ugene/position_weight_matrix/JASPAR/fungi/MA0286.1.pfm
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  286. share/ugene/position_weight_matrix/JASPAR/fungi/MA0290.1.pfm
  287. share/ugene/position_weight_matrix/JASPAR/fungi/MA0291.1.pfm
  288. share/ugene/position_weight_matrix/JASPAR/fungi/MA0292.1.pfm
  289. share/ugene/position_weight_matrix/JASPAR/fungi/MA0293.1.pfm
  290. share/ugene/position_weight_matrix/JASPAR/fungi/MA0294.1.pfm
  291. share/ugene/position_weight_matrix/JASPAR/fungi/MA0295.1.pfm
  292. share/ugene/position_weight_matrix/JASPAR/fungi/MA0296.1.pfm
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  295. share/ugene/position_weight_matrix/JASPAR/fungi/MA0299.1.pfm
  296. share/ugene/position_weight_matrix/JASPAR/fungi/MA0300.1.pfm
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  726. share/ugene/position_weight_matrix/UniPROBE/Cell08/Alx3_3418.2.pwm
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  728. share/ugene/position_weight_matrix/UniPROBE/Cell08/Arx_1738.2.pwm
  729. share/ugene/position_weight_matrix/UniPROBE/Cell08/Bapx1_2343.1.pwm
  730. share/ugene/position_weight_matrix/UniPROBE/Cell08/Barhl1_2590.2.pwm
  731. share/ugene/position_weight_matrix/UniPROBE/Cell08/Barhl2_3868.1.pwm
  732. share/ugene/position_weight_matrix/UniPROBE/Cell08/Barx1_2877.1.pwm
  733. share/ugene/position_weight_matrix/UniPROBE/Cell08/Barx2_3447.2.pwm
  734. share/ugene/position_weight_matrix/UniPROBE/Cell08/Bsx_3483.2.pwm
  735. share/ugene/position_weight_matrix/UniPROBE/Cell08/Cart1_0997.1.pwm
  736. share/ugene/position_weight_matrix/UniPROBE/Cell08/Cart1_1275.1.pwm
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  738. share/ugene/position_weight_matrix/UniPROBE/Cell08/Cdx2_4272.1.pwm
  739. share/ugene/position_weight_matrix/UniPROBE/Cell08/Cphx_3484.1.pwm
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  741. share/ugene/position_weight_matrix/UniPROBE/Cell08/Cutl1_3494.1.pwm
  742. share/ugene/position_weight_matrix/UniPROBE/Cell08/Cutl1_3494.2.pwm
  743. share/ugene/position_weight_matrix/UniPROBE/Cell08/Dbx1_3486.1.pwm
  744. share/ugene/position_weight_matrix/UniPROBE/Cell08/Dbx2_3487.1.pwm
  745. share/ugene/position_weight_matrix/UniPROBE/Cell08/Dlx1_1741.2.pwm
  746. share/ugene/position_weight_matrix/UniPROBE/Cell08/Dlx2_2273.2.pwm
  747. share/ugene/position_weight_matrix/UniPROBE/Cell08/Dlx3_1030.1.pwm
  748. share/ugene/position_weight_matrix/UniPROBE/Cell08/Dlx4_3488.2.pwm
  749. share/ugene/position_weight_matrix/UniPROBE/Cell08/Dlx5_3419.2.pwm
  750. share/ugene/position_weight_matrix/UniPROBE/Cell08/Dmbx1_2277.1.pwm
  751. share/ugene/position_weight_matrix/UniPROBE/Cell08/Dobox4_3956.2.pwm
  752. share/ugene/position_weight_matrix/UniPROBE/Cell08/Dobox5_3493.1.pwm
  753. share/ugene/position_weight_matrix/UniPROBE/Cell08/Duxl_1286.2.pwm
  754. share/ugene/position_weight_matrix/UniPROBE/Cell08/Emx2_3420.1.pwm
  755. share/ugene/position_weight_matrix/UniPROBE/Cell08/En1_3123.2.pwm
  756. share/ugene/position_weight_matrix/UniPROBE/Cell08/En2_0952.1.pwm
  757. share/ugene/position_weight_matrix/UniPROBE/Cell08/Esx1_3124.2.pwm
  758. share/ugene/position_weight_matrix/UniPROBE/Cell08/Evx1_3952.2.pwm
  759. share/ugene/position_weight_matrix/UniPROBE/Cell08/Evx2_2645.3.pwm
  760. share/ugene/position_weight_matrix/UniPROBE/Cell08/Gbx1_2883.2.pwm
  761. share/ugene/position_weight_matrix/UniPROBE/Cell08/Gbx2_3110.1.pwm
  762. share/ugene/position_weight_matrix/UniPROBE/Cell08/Gsc_2327.3.pwm
  763. share/ugene/position_weight_matrix/UniPROBE/Cell08/Gsh2_3990.2.pwm
  764. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hdx_3845.3.pwm
  765. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hlx1_2350.1.pwm
  766. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hlxb9_3422.1.pwm
  767. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hmbox1_2674.1.pwm
  768. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hmx1_3423.1.pwm
  769. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hmx2_3424.3.pwm
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  771. share/ugene/position_weight_matrix/UniPROBE/Cell08/Homez_1063.2.pwm
  772. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxa10_2318.1.pwm
  773. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxa11_2218.1.pwm
  774. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxa13_3126.1.pwm
  775. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxa1_3425.1.pwm
  776. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxa2_3079.1.pwm
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  778. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxa4_3426.1.pwm
  779. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxa5_3415.1.pwm
  780. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxa6_1040.1.pwm
  781. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxa7_2668.2.pwm
  782. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxa7_3750.1.pwm
  783. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxa9_2622.2.pwm
  784. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxb13_3479.1.pwm
  785. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxb3_1720.2.pwm
  786. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxb4_2627.1.pwm
  787. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxb5_3122.2.pwm
  788. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxb6_3428.2.pwm
  789. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxb7_3953.1.pwm
  790. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxb8_3780.2.pwm
  791. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxb9_3413.1.pwm
  792. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxc10_2779.2.pwm
  793. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxc11_3718.2.pwm
  794. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxc12_3480.1.pwm
  795. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxc13_3127.1.pwm
  796. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxc4_3491.1.pwm
  797. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxc5_2630.2.pwm
  798. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxc6_3954.2.pwm
  799. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxc8_3429.2.pwm
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  802. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxd11_3873.1.pwm
  803. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxd12_3481.1.pwm
  804. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxd13_2356.1.pwm
  805. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxd1_3448.1.pwm
  806. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxd3_1742.2.pwm
  807. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxd8_2644.1.pwm
  808. share/ugene/position_weight_matrix/UniPROBE/Cell08/Ipf1_3815.1.pwm
  809. share/ugene/position_weight_matrix/UniPROBE/Cell08/Irx2_0900.3.pwm
  810. share/ugene/position_weight_matrix/UniPROBE/Cell08/Irx3_0920.1.pwm
  811. share/ugene/position_weight_matrix/UniPROBE/Cell08/Irx3_2226.1.pwm
  812. share/ugene/position_weight_matrix/UniPROBE/Cell08/Irx4_2242.3.pwm
  813. share/ugene/position_weight_matrix/UniPROBE/Cell08/Irx5_2385.1.pwm
  814. share/ugene/position_weight_matrix/UniPROBE/Cell08/Irx6_2623.2.pwm
  815. share/ugene/position_weight_matrix/UniPROBE/Cell08/Isl2_3430.1.pwm
  816. share/ugene/position_weight_matrix/UniPROBE/Cell08/Isx_3445.1.pwm
  817. share/ugene/position_weight_matrix/UniPROBE/Cell08/Lbx2_3869.2.pwm
  818. share/ugene/position_weight_matrix/UniPROBE/Cell08/Lhx1_2240.2.pwm
  819. share/ugene/position_weight_matrix/UniPROBE/Cell08/Lhx2_0953.2.pwm
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  821. share/ugene/position_weight_matrix/UniPROBE/Cell08/Lhx4_1719.2.pwm
  822. share/ugene/position_weight_matrix/UniPROBE/Cell08/Lhx5_2279.1.pwm
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  824. share/ugene/position_weight_matrix/UniPROBE/Cell08/Lhx6_3432.1.pwm
  825. share/ugene/position_weight_matrix/UniPROBE/Cell08/Lhx8_2247.2.pwm
  826. share/ugene/position_weight_matrix/UniPROBE/Cell08/Lhx9_3492.1.pwm
  827. share/ugene/position_weight_matrix/UniPROBE/Cell08/Lmx1a_2238.2.pwm
  828. share/ugene/position_weight_matrix/UniPROBE/Cell08/Lmx1b_3433.2.pwm
  829. share/ugene/position_weight_matrix/UniPROBE/Cell08/Meis1_2335.1.pwm
  830. share/ugene/position_weight_matrix/UniPROBE/Cell08/Meox1_2310.2.pwm
  831. share/ugene/position_weight_matrix/UniPROBE/Cell08/Mrg1_2246.2.pwm
  832. share/ugene/position_weight_matrix/UniPROBE/Cell08/Mrg2_2302.1.pwm
  833. share/ugene/position_weight_matrix/UniPROBE/Cell08/Msx1_3031.2.pwm
  834. share/ugene/position_weight_matrix/UniPROBE/Cell08/Msx2_3449.1.pwm
  835. share/ugene/position_weight_matrix/UniPROBE/Cell08/Msx3_3206.1.pwm
  836. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx1-1_3856.3.pwm
  837. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx1-2_3214.1.pwm
  838. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx2-2_2823.1.pwm
  839. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx2-3_3435.1.pwm
  840. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx2-4_3074.1.pwm
  841. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx2-5_3436.1.pwm
  842. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx2-6_3437.1.pwm
  843. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx2-9_3082.1.pwm
  844. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx3-1_2923.2.pwm
  845. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx6-1_2825.1.pwm
  846. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx6-1_2825.2.pwm
  847. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx6-3_3446.1.pwm
  848. share/ugene/position_weight_matrix/UniPROBE/Cell08/Obox1_3970.2.pwm
  849. share/ugene/position_weight_matrix/UniPROBE/Cell08/Obox2_3438.2.pwm
  850. share/ugene/position_weight_matrix/UniPROBE/Cell08/Obox3_3439.1.pwm
  851. share/ugene/position_weight_matrix/UniPROBE/Cell08/Obox5_2284.1.pwm
  852. share/ugene/position_weight_matrix/UniPROBE/Cell08/Obox5_3963.2.pwm
  853. share/ugene/position_weight_matrix/UniPROBE/Cell08/Obox6_3440.2.pwm
  854. share/ugene/position_weight_matrix/UniPROBE/Cell08/Og2x_3719.1.pwm
  855. share/ugene/position_weight_matrix/UniPROBE/Cell08/Otp_3496.1.pwm
  856. share/ugene/position_weight_matrix/UniPROBE/Cell08/Otx1_2325.1.pwm
  857. share/ugene/position_weight_matrix/UniPROBE/Cell08/Otx2_3441.1.pwm
  858. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pax4_3989.2.pwm
  859. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pax6_3838.3.pwm
  860. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pax7_3783.1.pwm
  861. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pbx1_3203.1.pwm
  862. share/ugene/position_weight_matrix/UniPROBE/Cell08/Phox2a_3947.1.pwm
  863. share/ugene/position_weight_matrix/UniPROBE/Cell08/Phox2b_3948.1.pwm
  864. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pitx1_2312.1.pwm
  865. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pitx2_2274.3.pwm
  866. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pitx3_3497.2.pwm
  867. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pknox1_2364.2.pwm
  868. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pknox2_3077.2.pwm
  869. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou1f1_3818.1.pwm
  870. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou2f1_3081.2.pwm
  871. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou2f2_3748.1.pwm
  872. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou2f3_3986.2.pwm
  873. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou3f1_3819.1.pwm
  874. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou3f2_2824.1.pwm
  875. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou3f3_3235.2.pwm
  876. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou3f4_3773.1.pwm
  877. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou4f3_2791.1.pwm
  878. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou6f1_1731.2.pwm
  879. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou6f1_3733.1.pwm
  880. share/ugene/position_weight_matrix/UniPROBE/Cell08/Prop1_3949.1.pwm
  881. share/ugene/position_weight_matrix/UniPROBE/Cell08/Prrx1_3442.1.pwm
  882. share/ugene/position_weight_matrix/UniPROBE/Cell08/Prrx2_3072.1.pwm
  883. share/ugene/position_weight_matrix/UniPROBE/Cell08/Rax_3443.1.pwm
  884. share/ugene/position_weight_matrix/UniPROBE/Cell08/Rhox11_1765.2.pwm
  885. share/ugene/position_weight_matrix/UniPROBE/Cell08/Rhox11_2205.1.pwm
  886. share/ugene/position_weight_matrix/UniPROBE/Cell08/Rhox6_4251.1.pwm
  887. share/ugene/position_weight_matrix/UniPROBE/Cell08/Shox2_2641.2.pwm
  888. share/ugene/position_weight_matrix/UniPROBE/Cell08/Six1_0935.2.pwm
  889. share/ugene/position_weight_matrix/UniPROBE/Cell08/Six2_2307.2.pwm
  890. share/ugene/position_weight_matrix/UniPROBE/Cell08/Six3_1732.2.pwm
  891. share/ugene/position_weight_matrix/UniPROBE/Cell08/Six4_2860.1.pwm
  892. share/ugene/position_weight_matrix/UniPROBE/Cell08/Six6_2267.4.pwm
  893. share/ugene/position_weight_matrix/UniPROBE/Cell08/Six6_2267.5.pwm
  894. share/ugene/position_weight_matrix/UniPROBE/Cell08/Tcf1_2666.2.pwm
  895. share/ugene/position_weight_matrix/UniPROBE/Cell08/Tcf2_0913.2.pwm
  896. share/ugene/position_weight_matrix/UniPROBE/Cell08/Tgif1_2342.2.pwm
  897. share/ugene/position_weight_matrix/UniPROBE/Cell08/Tgif2_3451.1.pwm
  898. share/ugene/position_weight_matrix/UniPROBE/Cell08/Titf1_1722.2.pwm
  899. share/ugene/position_weight_matrix/UniPROBE/Cell08/Tlx2_3498.2.pwm
  900. share/ugene/position_weight_matrix/UniPROBE/Cell08/Uncx4.1_2281.2.pwm
  901. share/ugene/position_weight_matrix/UniPROBE/Cell08/Vax1_3499.1.pwm
  902. share/ugene/position_weight_matrix/UniPROBE/Cell08/Vax2_3500.1.pwm
  903. share/ugene/position_weight_matrix/UniPROBE/Cell08/Vsx1_1728.1.pwm
  904. share/ugene/position_weight_matrix/UniPROBE/GR09/Aft1.pwm
  905. share/ugene/position_weight_matrix/UniPROBE/GR09/Aro80.pwm
  906. share/ugene/position_weight_matrix/UniPROBE/GR09/Asg1.pwm
  907. share/ugene/position_weight_matrix/UniPROBE/GR09/Bas1.pwm
  908. share/ugene/position_weight_matrix/UniPROBE/GR09/Cbf1.pwm
  909. share/ugene/position_weight_matrix/UniPROBE/GR09/Cep3.pwm
  910. share/ugene/position_weight_matrix/UniPROBE/GR09/Cha4.pwm
  911. share/ugene/position_weight_matrix/UniPROBE/GR09/Cup9.pwm
  912. share/ugene/position_weight_matrix/UniPROBE/GR09/Ecm22.pwm
  913. share/ugene/position_weight_matrix/UniPROBE/GR09/Fhl1.pwm
  914. share/ugene/position_weight_matrix/UniPROBE/GR09/Fkh1.pwm
  915. share/ugene/position_weight_matrix/UniPROBE/GR09/Fkh2.pwm
  916. share/ugene/position_weight_matrix/UniPROBE/GR09/Gal4.pwm
  917. share/ugene/position_weight_matrix/UniPROBE/GR09/Gat1.pwm
  918. share/ugene/position_weight_matrix/UniPROBE/GR09/Gat3.pwm
  919. share/ugene/position_weight_matrix/UniPROBE/GR09/Gat4.pwm
  920. share/ugene/position_weight_matrix/UniPROBE/GR09/Gcn4.pwm
  921. share/ugene/position_weight_matrix/UniPROBE/GR09/Gln3.pwm
  922. share/ugene/position_weight_matrix/UniPROBE/GR09/Gsm1.pwm
  923. share/ugene/position_weight_matrix/UniPROBE/GR09/Gzf3.pwm
  924. share/ugene/position_weight_matrix/UniPROBE/GR09/Hal9.pwm
  925. share/ugene/position_weight_matrix/UniPROBE/GR09/Leu3.pwm
  926. share/ugene/position_weight_matrix/UniPROBE/GR09/Lys14.pwm
  927. share/ugene/position_weight_matrix/UniPROBE/GR09/Matalpha2.pwm
  928. share/ugene/position_weight_matrix/UniPROBE/GR09/Mbp1.pwm
  929. share/ugene/position_weight_matrix/UniPROBE/GR09/Mcm1.pwm
  930. share/ugene/position_weight_matrix/UniPROBE/GR09/Met32.pwm
  931. share/ugene/position_weight_matrix/UniPROBE/GR09/Mga1.pwm
  932. share/ugene/position_weight_matrix/UniPROBE/GR09/Mig1.pwm
  933. share/ugene/position_weight_matrix/UniPROBE/GR09/Mig2.pwm
  934. share/ugene/position_weight_matrix/UniPROBE/GR09/Mig3.pwm
  935. share/ugene/position_weight_matrix/UniPROBE/GR09/Ndt80.pwm
  936. share/ugene/position_weight_matrix/UniPROBE/GR09/Nhp6a.pwm
  937. share/ugene/position_weight_matrix/UniPROBE/GR09/Nhp6b.pwm
  938. share/ugene/position_weight_matrix/UniPROBE/GR09/Nrg1.pwm
  939. share/ugene/position_weight_matrix/UniPROBE/GR09/Oaf1.pwm
  940. share/ugene/position_weight_matrix/UniPROBE/GR09/Pbf1.pwm
  941. share/ugene/position_weight_matrix/UniPROBE/GR09/Pbf2.pwm
  942. share/ugene/position_weight_matrix/UniPROBE/GR09/Pdr1.pwm
  943. share/ugene/position_weight_matrix/UniPROBE/GR09/Phd1.pwm
  944. share/ugene/position_weight_matrix/UniPROBE/GR09/Pho2.pwm
  945. share/ugene/position_weight_matrix/UniPROBE/GR09/Pho4.pwm
  946. share/ugene/position_weight_matrix/UniPROBE/GR09/Put3.pwm
  947. share/ugene/position_weight_matrix/UniPROBE/GR09/Rap1.pwm
  948. share/ugene/position_weight_matrix/UniPROBE/GR09/Rdr1.pwm
  949. share/ugene/position_weight_matrix/UniPROBE/GR09/Rds1.pwm
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  951. share/ugene/position_weight_matrix/UniPROBE/GR09/Rgt1.pwm
  952. share/ugene/position_weight_matrix/UniPROBE/GR09/Rph1.pwm
  953. share/ugene/position_weight_matrix/UniPROBE/GR09/Rpn4.pwm
  954. share/ugene/position_weight_matrix/UniPROBE/GR09/Rsc3.pwm
  955. share/ugene/position_weight_matrix/UniPROBE/GR09/Rsc30.pwm
  956. share/ugene/position_weight_matrix/UniPROBE/GR09/Rtg3.pwm
  957. share/ugene/position_weight_matrix/UniPROBE/GR09/Sfl1.pwm
  958. share/ugene/position_weight_matrix/UniPROBE/GR09/Sfp1.pwm
  959. share/ugene/position_weight_matrix/UniPROBE/GR09/Sip4.pwm
  960. share/ugene/position_weight_matrix/UniPROBE/GR09/Skn7.pwm
  961. share/ugene/position_weight_matrix/UniPROBE/GR09/Smp1.pwm
  962. share/ugene/position_weight_matrix/UniPROBE/GR09/Spt15.pwm
  963. share/ugene/position_weight_matrix/UniPROBE/GR09/Srd1.pwm
  964. share/ugene/position_weight_matrix/UniPROBE/GR09/Stb3.pwm
  965. share/ugene/position_weight_matrix/UniPROBE/GR09/Stp2.pwm
  966. share/ugene/position_weight_matrix/UniPROBE/GR09/Stp4.pwm
  967. share/ugene/position_weight_matrix/UniPROBE/GR09/Sum1.pwm
  968. share/ugene/position_weight_matrix/UniPROBE/GR09/Sut2.pwm
  969. share/ugene/position_weight_matrix/UniPROBE/GR09/Tbf1.pwm
  970. share/ugene/position_weight_matrix/UniPROBE/GR09/Tbs1.pwm
  971. share/ugene/position_weight_matrix/UniPROBE/GR09/Tea1.pwm
  972. share/ugene/position_weight_matrix/UniPROBE/GR09/Tec1.pwm
  973. share/ugene/position_weight_matrix/UniPROBE/GR09/Tye7.pwm
  974. share/ugene/position_weight_matrix/UniPROBE/GR09/Ume6.pwm
  975. share/ugene/position_weight_matrix/UniPROBE/GR09/Usv1.pwm
  976. share/ugene/position_weight_matrix/UniPROBE/GR09/Xbp1.pwm
  977. share/ugene/position_weight_matrix/UniPROBE/GR09/Yap1.pwm
  978. share/ugene/position_weight_matrix/UniPROBE/GR09/Yap6.pwm
  979. share/ugene/position_weight_matrix/UniPROBE/GR09/Ybr239c.pwm
  980. share/ugene/position_weight_matrix/UniPROBE/GR09/Ydr520c.pwm
  981. share/ugene/position_weight_matrix/UniPROBE/GR09/Yer130c.pwm
  982. share/ugene/position_weight_matrix/UniPROBE/GR09/Ygr067c.pwm
  983. share/ugene/position_weight_matrix/UniPROBE/GR09/Ykl222c.pwm
  984. share/ugene/position_weight_matrix/UniPROBE/GR09/Yll054c.pwm
  985. share/ugene/position_weight_matrix/UniPROBE/GR09/Yml081w.pwm
  986. share/ugene/position_weight_matrix/UniPROBE/GR09/Ynr063w.pwm
  987. share/ugene/position_weight_matrix/UniPROBE/GR09/Yox1.pwm
  988. share/ugene/position_weight_matrix/UniPROBE/GR09/Ypr013c.pwm
  989. share/ugene/position_weight_matrix/UniPROBE/GR09/Ypr015c.pwm
  990. share/ugene/position_weight_matrix/UniPROBE/GR09/Ypr196w.pwm
  991. share/ugene/position_weight_matrix/UniPROBE/GR09/Yrm1.pwm
  992. share/ugene/position_weight_matrix/UniPROBE/GR09/Yrr1.pwm
  993. share/ugene/position_weight_matrix/UniPROBE/NBT06/Cbf1.pwm
  994. share/ugene/position_weight_matrix/UniPROBE/NBT06/Ceh-22.pwm
  995. share/ugene/position_weight_matrix/UniPROBE/NBT06/Oct-1.pwm
  996. share/ugene/position_weight_matrix/UniPROBE/NBT06/Rap1.pwm
  997. share/ugene/position_weight_matrix/UniPROBE/NBT06/Zif268.pwm
  998. share/ugene/position_weight_matrix/UniPROBE/PNAS08/Cgd2_3490.pwm
  999. share/ugene/position_weight_matrix/UniPROBE/PNAS08/PF14_0633.pwm
  1000. share/ugene/position_weight_matrix/UniPROBE/PNAS08/PFF0200c.pwm
  1001. share/ugene/position_weight_matrix/UniPROBE/all_uniprobe.csv
  1002. share/ugene/primer3/drosophila.w.transposons.txt
  1003. share/ugene/primer3/humrep_and_simple.txt
  1004. share/ugene/primer3/rodent_ref.txt
  1005. share/ugene/primer3/rodrep_and_simple.txt
  1006. share/ugene/query_samples/RepeatsWithORF.uql
  1007. share/ugene/query_samples/SimpleGene.uql
  1008. share/ugene/samples/ABIF/A01.abi
  1009. share/ugene/samples/ACE/BL060C3.ace
  1010. share/ugene/samples/ACE/K26.ace
  1011. share/ugene/samples/APR/DNA.apr
  1012. share/ugene/samples/APR/gyrA.apr
  1013. share/ugene/samples/Assembly/chrM.fa
  1014. share/ugene/samples/Assembly/chrM.sam
  1015. share/ugene/samples/Assembly/chrM.sorted.bam
  1016. share/ugene/samples/CLUSTALW/COI.aln
  1017. share/ugene/samples/CLUSTALW/HIV-1.aln
  1018. share/ugene/samples/CLUSTALW/ty3.aln.gz
  1019. share/ugene/samples/EMBL/AF177870.emb
  1020. share/ugene/samples/EMBL/AL000263.emb
  1021. share/ugene/samples/FASTA/human_T1.fa
  1022. share/ugene/samples/FASTQ/eas.fastq
  1023. share/ugene/samples/GFF/5prime_utr_intron_A20.gff
  1024. share/ugene/samples/GFF/5prime_utr_intron_A21.gff
  1025. share/ugene/samples/Genbank/CVU55762.gb
  1026. share/ugene/samples/Genbank/NC_014267.1.gb
  1027. share/ugene/samples/Genbank/PBR322.gb
  1028. share/ugene/samples/Genbank/murine.gb
  1029. share/ugene/samples/Genbank/sars.gb
  1030. share/ugene/samples/HMM/aligment15900.hmm
  1031. share/ugene/samples/MMDB/1CRN.prt
  1032. share/ugene/samples/MMDB/2JQS.prt
  1033. share/ugene/samples/MSF/HMA.msf
  1034. share/ugene/samples/MSF/lipid8.msf
  1035. share/ugene/samples/MSF/pla2_20.msf
  1036. share/ugene/samples/Newick/COI.nwk
  1037. share/ugene/samples/PDB/1CF7.PDB
  1038. share/ugene/samples/PDB/1CRN.PDB
  1039. share/ugene/samples/PDB/3INS.PDB
  1040. share/ugene/samples/Raw/raw.seq
  1041. share/ugene/samples/SCF/90-JRI-07.scf
  1042. share/ugene/samples/Sanger/alignment.ugenedb
  1043. share/ugene/samples/Stockholm/CBS.sto
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  1045. share/ugene/samples/Swiss-Prot/D0VTW9.txt
  1046. share/ugene/samples/Swiss-Prot/P01375.txt
  1047. share/ugene/samples/Swiss-Prot/P16152.txt
  1048. share/ugene/sitecon_models/eukaryotic/CEBP_a.sitecon.gz
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  1125. share/ugene/sitecon_models/prokaryotic/NAC.sitecon.gz
  1126. share/ugene/sitecon_models/prokaryotic/NAGC_new2.sitecon.gz
  1127. share/ugene/sitecon_models/prokaryotic/NANR.sitecon.gz
  1128. share/ugene/sitecon_models/prokaryotic/NARL2.sitecon.gz
  1129. share/ugene/sitecon_models/prokaryotic/NARP.sitecon.gz
  1130. share/ugene/sitecon_models/prokaryotic/NTRC.sitecon.gz
  1131. share/ugene/sitecon_models/prokaryotic/NarL.sitecon.gz
  1132. share/ugene/sitecon_models/prokaryotic/OmpR.sitecon.gz
  1133. share/ugene/sitecon_models/prokaryotic/OxyR.sitecon.gz
  1134. share/ugene/sitecon_models/prokaryotic/PHOB.sitecon.gz
  1135. share/ugene/sitecon_models/prokaryotic/PHOP.sitecon.gz
  1136. share/ugene/sitecon_models/prokaryotic/PurR.sitecon.gz
  1137. share/ugene/sitecon_models/prokaryotic/ROB.sitecon.gz
  1138. share/ugene/sitecon_models/prokaryotic/RcsB_1core.sitecon.gz
  1139. share/ugene/sitecon_models/prokaryotic/RcsB_2core.sitecon.gz
  1140. share/ugene/sitecon_models/prokaryotic/Rob2.sitecon.gz
  1141. share/ugene/sitecon_models/prokaryotic/TORR.sitecon.gz
  1142. share/ugene/sitecon_models/prokaryotic/TRPR.sitecon.gz
  1143. share/ugene/sitecon_models/prokaryotic/TyrR.sitecon.gz
  1144. share/ugene/sitecon_models/prokaryotic/fis_new1.sitecon.gz
  1145. share/ugene/sitecon_models/prokaryotic/soxS.sitecon.gz
  1146. share/ugene/snp_scripts/SNPChIPTools.py
  1147. share/ugene/snp_scripts/pdb_uniprot_chain_map.lst.2
  1148. share/ugene/snp_scripts/protstability1d.py
  1149. share/ugene/snp_scripts/protstability3d.py
  1150. share/ugene/snp_scripts/rsnp.py
  1151. share/ugene/snp_scripts/snp2pdbsite.py
  1152. share/ugene/snp_scripts/update_d_db.py
  1153. share/ugene/translations.txt
  1154. share/ugene/weight_matrix/blosum100.txt
  1155. share/ugene/weight_matrix/blosum30.txt
  1156. share/ugene/weight_matrix/blosum35.txt
  1157. share/ugene/weight_matrix/blosum40.txt
  1158. share/ugene/weight_matrix/blosum45.txt
  1159. share/ugene/weight_matrix/blosum50.txt
  1160. share/ugene/weight_matrix/blosum55.txt
  1161. share/ugene/weight_matrix/blosum60.txt
  1162. share/ugene/weight_matrix/blosum62.txt
  1163. share/ugene/weight_matrix/blosum65.txt
  1164. share/ugene/weight_matrix/blosum70.txt
  1165. share/ugene/weight_matrix/blosum75.txt
  1166. share/ugene/weight_matrix/blosum80.txt
  1167. share/ugene/weight_matrix/blosum85.txt
  1168. share/ugene/weight_matrix/blosum90.txt
  1169. share/ugene/weight_matrix/blosumn.txt
  1170. share/ugene/weight_matrix/dayhoff.txt
  1171. share/ugene/weight_matrix/dna.txt
  1172. share/ugene/weight_matrix/gonnet.txt
  1173. share/ugene/weight_matrix/identity.txt
  1174. share/ugene/weight_matrix/match.txt
  1175. share/ugene/weight_matrix/md_10.txt
  1176. share/ugene/weight_matrix/md_20.txt
  1177. share/ugene/weight_matrix/md_40.txt
  1178. share/ugene/weight_matrix/nuc.4.4.txt
  1179. share/ugene/weight_matrix/pam10.txt
  1180. share/ugene/weight_matrix/pam100.txt
  1181. share/ugene/weight_matrix/pam110.txt
  1182. share/ugene/weight_matrix/pam120.cdi.txt
  1183. share/ugene/weight_matrix/pam120.txt
  1184. share/ugene/weight_matrix/pam130.txt
  1185. share/ugene/weight_matrix/pam140.txt
  1186. share/ugene/weight_matrix/pam150.txt
  1187. share/ugene/weight_matrix/pam160.cdi.txt
  1188. share/ugene/weight_matrix/pam160.txt
  1189. share/ugene/weight_matrix/pam170.txt
  1190. share/ugene/weight_matrix/pam180.txt
  1191. share/ugene/weight_matrix/pam190.txt
  1192. share/ugene/weight_matrix/pam20.txt
  1193. share/ugene/weight_matrix/pam200.cdi.txt
  1194. share/ugene/weight_matrix/pam200.txt
  1195. share/ugene/weight_matrix/pam210.txt
  1196. share/ugene/weight_matrix/pam220.txt
  1197. share/ugene/weight_matrix/pam230.txt
  1198. share/ugene/weight_matrix/pam240.txt
  1199. share/ugene/weight_matrix/pam250.cdi.txt
  1200. share/ugene/weight_matrix/pam250.txt
  1201. share/ugene/weight_matrix/pam260.txt
  1202. share/ugene/weight_matrix/pam270.txt
  1203. share/ugene/weight_matrix/pam280.txt
  1204. share/ugene/weight_matrix/pam290.txt
  1205. share/ugene/weight_matrix/pam30.txt
  1206. share/ugene/weight_matrix/pam300.txt
  1207. share/ugene/weight_matrix/pam310.txt
  1208. share/ugene/weight_matrix/pam320.txt
  1209. share/ugene/weight_matrix/pam330.txt
  1210. share/ugene/weight_matrix/pam340.txt
  1211. share/ugene/weight_matrix/pam350.txt
  1212. share/ugene/weight_matrix/pam360.txt
  1213. share/ugene/weight_matrix/pam370.txt
  1214. share/ugene/weight_matrix/pam380.txt
  1215. share/ugene/weight_matrix/pam390.txt
  1216. share/ugene/weight_matrix/pam40.cdi.txt
  1217. share/ugene/weight_matrix/pam40.txt
  1218. share/ugene/weight_matrix/pam400.txt
  1219. share/ugene/weight_matrix/pam410.txt
  1220. share/ugene/weight_matrix/pam420.txt
  1221. share/ugene/weight_matrix/pam430.txt
  1222. share/ugene/weight_matrix/pam440.txt
  1223. share/ugene/weight_matrix/pam450.txt
  1224. share/ugene/weight_matrix/pam460.txt
  1225. share/ugene/weight_matrix/pam470.txt
  1226. share/ugene/weight_matrix/pam480.txt
  1227. share/ugene/weight_matrix/pam490.txt
  1228. share/ugene/weight_matrix/pam50.txt
  1229. share/ugene/weight_matrix/pam500.txt
  1230. share/ugene/weight_matrix/pam60.txt
  1231. share/ugene/weight_matrix/pam70.txt
  1232. share/ugene/weight_matrix/pam80.cdi.txt
  1233. share/ugene/weight_matrix/pam80.txt
  1234. share/ugene/weight_matrix/pam90.txt
  1235. share/ugene/weight_matrix/rna.txt
  1236. share/ugene/weight_matrix/vtml160.txt
  1237. share/ugene/weight_matrix/vtml200.txt
  1238. share/ugene/workflow_samples/Alignment/basic_align.uwl
  1239. share/ugene/workflow_samples/Alignment/extract_msa_consensus_as_seq.uwl
  1240. share/ugene/workflow_samples/Alignment/extract_msa_consensus_as_text.uwl
  1241. share/ugene/workflow_samples/Conversions/faqual2fastq.uwl
  1242. share/ugene/workflow_samples/Conversions/msa2clustal.uwl
  1243. share/ugene/workflow_samples/Conversions/query2alignment.uwl
  1244. share/ugene/workflow_samples/Conversions/seq2gen.uwl
  1245. share/ugene/workflow_samples/Custom elements/casava-fastq-filter.uwl
  1246. share/ugene/workflow_samples/Custom elements/fastq-trimmer.uwl
  1247. share/ugene/workflow_samples/Custom elements/script-dump-sequence-info.uwl
  1248. share/ugene/workflow_samples/Custom elements/script-linkdata-fetch-seq.uwl
  1249. share/ugene/workflow_samples/Custom elements/script-quality-filter.uwl
  1250. share/ugene/workflow_samples/Data marking/annotation_marker.uwl
  1251. share/ugene/workflow_samples/Data marking/length_marker.uwl
  1252. share/ugene/workflow_samples/Data merging/find-substrings.uwl
  1253. share/ugene/workflow_samples/Data merging/merge-sequence.uwl
  1254. share/ugene/workflow_samples/Data merging/tfbs.uwl
  1255. share/ugene/workflow_samples/HMMER/build-test-HMM.uwl
  1256. share/ugene/workflow_samples/HMMER/searchHMM.uwl
  1257. share/ugene/workflow_samples/NGS/chipseq_coverage.uwl
  1258. share/ugene/workflow_samples/NGS/cistrome.uwl
  1259. share/ugene/workflow_samples/NGS/cistrome/chip_seq.uwl
  1260. share/ugene/workflow_samples/NGS/cistrome/chip_seq_with_control.uwl
  1261. share/ugene/workflow_samples/NGS/consensus.uwl
  1262. share/ugene/workflow_samples/NGS/extract_coverage.uwl
  1263. share/ugene/workflow_samples/NGS/extract_transcript_seq.uwl
  1264. share/ugene/workflow_samples/NGS/fastqc.uwl
  1265. share/ugene/workflow_samples/NGS/from_tools_menu_only/ngs_assembly.uwl
  1266. share/ugene/workflow_samples/NGS/from_tools_menu_only/ngs_classification.uwl
  1267. share/ugene/workflow_samples/NGS/ngs_assembly_illumina_pe.uwl
  1268. share/ugene/workflow_samples/NGS/ngs_assembly_illumina_pe_nanopore.uwl
  1269. share/ugene/workflow_samples/NGS/ngs_assembly_illumina_se.uwl
  1270. share/ugene/workflow_samples/NGS/ngs_classification/ngs_classification_de_novo/ngs_classification_de_novo_paired.uwl
  1271. share/ugene/workflow_samples/NGS/ngs_classification/ngs_classification_de_novo/ngs_classification_de_novo_single.uwl
  1272. share/ugene/workflow_samples/NGS/ngs_classification/ngs_classification_parallel/ngs_classification_parallel_paired.uwl
  1273. share/ugene/workflow_samples/NGS/ngs_classification/ngs_classification_parallel/ngs_classification_parallel_single.uwl
  1274. share/ugene/workflow_samples/NGS/ngs_classification/ngs_classification_serial/ngs_classification_serial_paired.uwl
  1275. share/ugene/workflow_samples/NGS/ngs_classification/ngs_classification_serial/ngs_classification_serial_single.uwl
  1276. share/ugene/workflow_samples/NGS/ngs_classification_de_novo.uwl
  1277. share/ugene/workflow_samples/NGS/ngs_classification_parallel.uwl
  1278. share/ugene/workflow_samples/NGS/ngs_classification_serial.uwl
  1279. share/ugene/workflow_samples/NGS/ngs_transcriptomics_tophat_stringtie.uwl
  1280. share/ugene/workflow_samples/NGS/ngs_transcriptomics_tuxedo.uwl
  1281. share/ugene/workflow_samples/NGS/ngs_variant_annotation.uwl
  1282. share/ugene/workflow_samples/NGS/ngs_variant_calling.uwl
  1283. share/ugene/workflow_samples/NGS/ngs_variant_calling_full.uwl
  1284. share/ugene/workflow_samples/NGS/raw_chip.uwl
  1285. share/ugene/workflow_samples/NGS/raw_dna.uwl
  1286. share/ugene/workflow_samples/NGS/raw_ngs/chipseq/chipseq_paired.uwl
  1287. share/ugene/workflow_samples/NGS/raw_ngs/chipseq/chipseq_single.uwl
  1288. share/ugene/workflow_samples/NGS/raw_ngs/dnaseq/dna_paired.uwl
  1289. share/ugene/workflow_samples/NGS/raw_ngs/dnaseq/dna_single.uwl
  1290. share/ugene/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_filtration_paired.uwl
  1291. share/ugene/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_filtration_single.uwl
  1292. share/ugene/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_paired.uwl
  1293. share/ugene/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_single.uwl
  1294. share/ugene/workflow_samples/NGS/raw_rna.uwl
  1295. share/ugene/workflow_samples/NGS/tuxedo/tuxedo_main.uwl
  1296. share/ugene/workflow_samples/NGS/tuxedo/tuxedo_main_paired.uwl
  1297. share/ugene/workflow_samples/NGS/tuxedo/tuxedo_no_novel_transcr.uwl
  1298. share/ugene/workflow_samples/NGS/tuxedo/tuxedo_no_novel_transcr_paired.uwl
  1299. share/ugene/workflow_samples/NGS/tuxedo/tuxedo_single_dataset.uwl
  1300. share/ugene/workflow_samples/NGS/tuxedo/tuxedo_single_dataset_paired.uwl
  1301. share/ugene/workflow_samples/NGS/unmapped_reads.uwl
  1302. share/ugene/workflow_samples/Sanger sequencing/trim-and-align.uwl
  1303. share/ugene/workflow_samples/Scenarios/filter_matched.uwl
  1304. share/ugene/workflow_samples/Scenarios/find_inverted_repeats.uwl
  1305. share/ugene/workflow_samples/Scenarios/find_sequences.uwl
  1306. share/ugene/workflow_samples/Scenarios/gene_by_gene_report.uwl
  1307. share/ugene/workflow_samples/Scenarios/group_primers_pairs.uwl
  1308. share/ugene/workflow_samples/Scenarios/intersect_annotations.uwl
  1309. share/ugene/workflow_samples/Scenarios/length_filter.uwl
  1310. share/ugene/workflow_samples/Scenarios/merge_sequence_annotation.uwl
  1311. share/ugene/workflow_samples/Scenarios/pcr.uwl
  1312. share/ugene/workflow_samples/Scenarios/remote_blasting.uwl
  1313. share/ugene/workflow_samples/Scenarios/translate_seq_and_compl.uwl
  1314. share/ugene/workflow_samples/Transcriptomics/SearchTFBS.uwl
  1315. share/ugene/workflow_samples/users/CASAVA FASTQ filter.usa
  1316. share/ugene/workflow_samples/users/Dump sequence info.usa
  1317. share/ugene/workflow_samples/users/FASTQ Trimmer.usa
  1318. share/ugene/workflow_samples/users/Get the first half of sequence.usa
  1319. share/ugene/workflow_samples/users/Get the second half of sequence.usa
  1320. share/ugene/workflow_samples/users/LengthMarker.usa
  1321. share/ugene/workflow_samples/users/LinkData Fetch.usa
  1322. share/ugene/workflow_samples/users/QualityFilter.usa
  1323. share/ugene/workflow_samples/users/Read one sequence.usa
  1324. @owner
  1325. @group
  1326. @mode
Collapse this list.
Dependency lines:
  • ugene>0:biology/ugene
To install the port: cd /usr/ports/biology/ugene/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/ugene
  • pkg install ugene
PKGNAME: ugene
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
ugene
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd64--
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64--
FreeBSD:12:amd6440.040.0
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i38640.140.0
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd6440.140.0
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i38640.140.0
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch64--
FreeBSD:14:amd6440.1-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i38640.1-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. update-desktop-database : devel/desktop-file-utils
  2. update-mime-database : misc/shared-mime-info
  3. xorgproto>=0 : x11/xorgproto
  4. xorgproto>=0 : x11/xorgproto
  5. x11.pc : x11/libX11
  6. xtst.pc : x11/libXtst
  7. qt5-buildtools>=5.15.2 : devel/qt5-buildtools
  8. lrelease : devel/qt5-linguisttools
  9. qt5-qmake>=5.15.2 : devel/qt5-qmake
Runtime dependencies:
  1. bash : shells/bash
  2. update-desktop-database : devel/desktop-file-utils
  3. update-mime-database : misc/shared-mime-info
  4. x11.pc : x11/libX11
  5. xtst.pc : x11/libXtst
  6. libqtiff.so : graphics/qt5-imageformats
Library dependencies:
  1. libGL.so : graphics/libglvnd
  2. libGLU.so : graphics/libGLU
  3. libsqlite3.so : databases/sqlite3
  4. libQt5Core.so : devel/qt5-core
  5. libQt5Gui.so : x11-toolkits/qt5-gui
  6. libQt5Network.so : net/qt5-network
  7. libQt5OpenGL.so : graphics/qt5-opengl
  8. libQt5PrintSupport.so : print/qt5-printsupport
  9. libQt5Script.so : devel/qt5-script
  10. libQt5ScriptTools.so : devel/qt5-scripttools
  11. libQt5Sql.so : databases/qt5-sql
  12. libQt5Svg.so : graphics/qt5-svg
  13. libQt5Test.so : devel/qt5-testlib
  14. libQt5Widgets.so : x11-toolkits/qt5-widgets
  15. libQt5Xml.so : textproc/qt5-xml
There are no ports dependent upon this port

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/ugeneunipro/ugene/tar.gz/40.1?dummy=/
Collapse this list.

Number of commits found: 53

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
14 Oct 2021 11:23:37
 files touched by this commit commit hash:e409be37a880805890a6a3ba0be4aed22042f25b  40.1
danfe search for other commits by this committer
biology/ugene: update UniPro UGENE to version 40.1 (bugfix release).
16 Sep 2021 09:48:26
 files touched by this commit commit hash:299862ff2afc17f5a415843ba9fc87ee6074fa87  40.0
danfe search for other commits by this committer
biology/ugene: update Unipro UGENE to version 40.0.
25 Jun 2021 17:56:47
 files touched by this commit commit hash:05f96c80f8f5cde88a25a3f71a1b6248dd84827a  39.0
danfe search for other commits by this committer
biology/ugene: update Unipro UGENE to version 39.0.
22 Jun 2021 18:53:08
 files touched by this commit commit hash:da3162c7c9f01912ba1940e188b253f2b5c7ba77  38.1_1
kbowling search for other commits by this committer
graphics/mesa-libs: Bump reverse deps for libglvnd

Per discussion with bapt on helping pkg handle the changing of these
deps and avoiding impossible upgrade senarios.

PR:		246767
Reviewed by:	manu, bapt
Approved by:	x11
Differential Revision:	https://reviews.freebsd.org/D30824
18 May 2021 15:24:55
 files touched by this commit commit hash:6464fe05fe9d896e130503dfc4533d946d787e0f  38.1
danfe search for other commits by this committer
- Update Unipro UGENE to version 38.1 and thus unbreak
- CONFIG defaults to 64-bit mode now, adjust the check
12 May 2021 11:55:32
 files touched by this commit commit hash:4b5a5c6d9c8767e327824d8d20c8d4bf86534904  38.0
amdmi3 search for other commits by this committer
biology/ugene: mark BROKEN (does not fetch)

Approved by:	portmgr blanket
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  38.0
mat search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
23 Mar 2021 14:20:49
Original commit files touched by this commit Revision:569026  38.0
danfe search for other commits by this committer
- Update Unipro UGENE to version 38.0
- Garbage-collect no longer needed patches
- Make COMMENT shorter and closer to upstream
- Stop building bundled SQLite, use ours!
19 Jan 2021 02:29:16
Original commit files touched by this commit Revision:562006  37.0
linimon search for other commits by this committer
Mark BROKEN on riscv64 the same as on aarch64.

While here, pet portlint (Makevar order).

Approved by:	portmgr (tier-2 blanket)
Obtained from:	lonesome.com build testing
31 Dec 2020 13:43:10
Original commit files touched by this commit Revision:559737  37.0
danfe search for other commits by this committer
- Update Unipro UGENE port to version 37.0
- Drop no longer used WebEngine dependencies
- Force SSE2 on i386 (required for the build)
- Chase HTTP 301 redirection in the WWW line
19 May 2020 18:00:02
Original commit files touched by this commit Revision:535875  34.0
tcberner search for other commits by this committer
biology/ugene: prepare for Qt5-5.15
10 May 2020 15:42:33
Original commit files touched by this commit Revision:534852  34.0
danfe search for other commits by this committer
- Resurrect and unbreak by updating to version 34.0
- Stop providing outdated offline PDF documentation,
  users are advised to use the online files instead
05 May 2020 15:38:12
Original commit files touched by this commit Revision:534093  1.31.0_1
rene search for other commits by this committer
Remove expired ports:

Adjusted for ports rescued since r534032

2020-05-05 audio/festvox-czech: Broken for more than 6 months
2020-05-05 audio/gkrellmvolume2: Broken for more than 6 months
2020-05-05 audio/mixmos: Broken for more than 6 months
2020-05-05 audio/mma: Broken for more than 6 months
2020-05-05 audio/pd-cyclone: Broken for more than 6 months
2020-05-05 audio/shorten: Broken for more than 6 months
2020-05-05 audio/taglib-sharp: Broken for more than 6 months
2020-05-05 audio/xhippo: Broken for more than 6 months
2020-05-05 biology/consed: Broken for more than 6 months
2020-05-05 biology/plinkseq: Broken for more than 6 months
2020-05-05 biology/seqtools: Broken for more than 6 months
(Only the first 15 lines of the commit message are shown above View all of this commit message)
04 Apr 2020 20:51:41
Original commit files touched by this commit Revision:530719  1.31.0_1  Sanity Test Failure
antoine search for other commits by this committer
Deprecate ports broken for more than 6 months
06 Nov 2019 12:48:32
Original commit files touched by this commit Revision:516880  1.31.0_1  Sanity Test Failure
antoine search for other commits by this committer
Mark a few ports BROKEN, unfetchable
04 Nov 2019 21:08:20
Original commit files touched by this commit Revision:516742  1.31.0_1
zeising search for other commits by this committer
Add USES=xorg USES=gl, ports categories b

Add USES=xorg, USES=gl and in a few cases USES=gnome to ports in categories
starting with 'b'.
16 Jan 2019 11:13:45
Original commit files touched by this commit Revision:490472  1.31.0_1
tijl search for other commits by this committer
Fix Qt5 symbol version scripts to put the catch-all clause first.  When
a symbol matches multiple clauses the last one takes precedence.  If the
catch-all is last it captures everything.  In the case of Qt5 libraries
this caused all symbols to have a Qt_5 label while some should have
Qt_5_PRIVATE_API.  This only affects lld because GNU ld always gives the
catch-all lowest priority.

Older versions of Qt5Webengine exported some memory allocation symbols from
the bundled Chromium.  Version 5.9 stopped exporting these [1] but the
symbols were kept as weak wrappers for the standard allocation functions to
maintain binary compatibility. [2][3]  The problem is that the call to the
standard function in these weak wrappers is only resolved to the standard
function if there's a call to this standard function in other parts of
Qt5Webengine, because only then is there a non-weak symbol that takes
precedence over the weak one.  If there's no such non-weak symbol the call
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16 Dec 2018 14:49:16
Original commit files touched by this commit Revision:487594  1.31.0
tcberner search for other commits by this committer
Update Qt5 to 5.12.0

http://blog.qt.io/blog/2018/12/06/qt-5-12-lts-released/

- This breaks support for libressl again. Patches are welcome.

PR:		233705
Exp-run by:	antoine
02 Sep 2018 20:47:15
Original commit files touched by this commit Revision:478818  1.31.0
jhale search for other commits by this committer
Update to 1.31.0

PR:		229463
Approved by:	Hannes Hauswedell <h2+fbsdports@fsfe.org> (maintainer)
28 Jun 2018 17:39:55
Original commit files touched by this commit Revision:473503  1.22.0_3
tcberner search for other commits by this committer
Replace bsd.qt.mk by Uses/qt.mk and Uses/qt-dist.mk

From now on, ports that depend on Qt4 will have to set
	USES=		qt:4
	USE_QT=		foo bar
ports depending on Qt5 will use
	USES=		qt:5
	USE_QT=		foo bar

PR:		229225
Exp-run by:	antoine
Reviewed by:	mat
Approved by:	portmgr (antoine)
Differential Revision:	-https://reviews.freebsd.org/D15540
15 May 2018 18:51:51
Original commit files touched by this commit Revision:470045  1.22.0_3
rakuco search for other commits by this committer
Add upstream patch to fix the build with Qt 5.10.

    _tmp/ui/ui_Bowtie2Settings.h:189:35: error: no viable conversion from
'QLatin1String' to 'const QKeySequence'
            gbarCheckBox->setShortcut(QLatin1String(""));
                                      ^~~~~~~~~~~~~~~~~

PR:		228213
06 Jan 2018 21:30:33
Original commit files touched by this commit Revision:458293  1.22.0_2
rakuco search for other commits by this committer
Update Qt5 ports to 5.9.3.

This took quite a lot of time because Qt's own build system underwent
several changes in 5.8.0 that took a while to adapt to.

And, of course, qt5-webengine is a behemoth that we need to patch like crazy
due to its bundling of Chromium. In fact, most of the Chromium patches in
qt5-webengine have been imported with no changes from www/chromium@433510
("www/chromium: update to 56.0.2924.87").

New port: accessibility/qt5-speech

Bigger changes to Qt5 ports we had to make:
- Qt now allows using a configure.json file to define configuration options
  and specify configuration checks that can be done when qmake is invoked.
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22 Sep 2017 10:48:29
Original commit files touched by this commit Revision:450351  1.22.0_2
mat search for other commits by this committer
Remove USES=execinfo.

PR:		220271
Submitted by:	mat (review), Yasuhiro KIMURA (PR)
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D11488
23 May 2017 05:03:16
Original commit files touched by this commit Revision:441503  1.22.0_2
rezny search for other commits by this committer
Revision bump of all ports with USE_GL after consolidation of mesa-libs

Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D10845
09 Jan 2017 13:16:50
Original commit files touched by this commit Revision:430947  1.22.0_1
amdmi3 search for other commits by this committer
- Remove always-true/false conditions after FreeBSD 9, 10.1, 10.2 EOL

Approved by:	portmgr blanket
08 Nov 2016 19:29:57
Original commit files touched by this commit Revision:425758  1.22.0_1
linimon search for other commits by this committer
The 64-bit arm arch is actually spelled 'aarch64', not 'arm64'.
08 Nov 2016 07:20:38
Original commit files touched by this commit Revision:425689  1.22.0_1
linimon search for other commits by this committer
Mark as broken on arm64.

Approved by:	portmgr (tier-2 blanket)
07 May 2016 19:38:53
Original commit files touched by this commit Revision:414784  1.22.0_1
dim search for other commits by this committer
During the exp-run in bug 208158, it was found that biology/ugene gives
errors with libc++ 3.8.0:

In file included from src/QScoreAdapter.cpp:1:
In file included from src/QScoreAdapter.h:4:
In file included from ../../include/U2Core/MAlignment.h:1:
In file included from
../../include/U2Core/../../corelibs/U2Core/src/datatype/MAlignment.h:25:
In file included from
../../include/U2Core/../../corelibs/U2Core/src/datatype/MAlignmentInfo.h:25:
In file included from /usr/local/include/qt5/QtCore/QString:1:
In file included from /usr/local/include/qt5/QtCore/qstring.h:41:
In file included from /usr/local/include/qt5/QtCore/qchar.h:37:
In file included from /usr/local/include/qt5/QtCore/qglobal.h:39:
/usr/include/c++/v1/cstddef:43:15: fatal error: 'stddef.h' file not found
#include_next <stddef.h>
              ^

This is because the port tries to add /usr/include as a system include
directory, using -isystem, and this screws up the order of include
directories.  Fix it by patching up a number of .pri files to avoid
using the -isystem flag.

Approved by:	h2+fbsdports@fsfe.org (maintainer)
PR:		209366
MFH:		2016Q2
14 Apr 2016 04:07:44
Original commit files touched by this commit Revision:413242  1.22.0
danfe search for other commits by this committer
Update to version 1.22.0, which now unfortunately requires Qt 5.x.  Also
since around v1.18.0, UGENE is using Google's Breakpad library for crash
reporting, which is very system-specific and does not support FreeBSD at
the moment.  Due to lack of resources and interest in porting it, simply
disable crash reporting code for the time being.
01 Apr 2016 13:29:17
Original commit files touched by this commit Revision:412344  1.17.0_1
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
18 Aug 2015 20:02:46
Original commit files touched by this commit Revision:394652  1.17.0_1
pgollucci search for other commits by this committer
biology/ugene: qt4-linguist -> qt4-linguisttools

- add USES=desktop-file-utils

PR:                  202138
Submitted by:        s3erios@gmail.com
Approved by:         h2+fbsdports@fsfe.org
15 Jul 2015 07:18:09
Original commit files touched by this commit Revision:392119  1.17.0
danfe search for other commits by this committer
- Update Unipro UGENE to version 1.17.0 (documentation was also rerolled)
- Remove no longer required local source code tweaks (picked up upstream)
28 May 2015 08:12:00
Original commit files touched by this commit Revision:387709  1.16.2
danfe search for other commits by this committer
Update Unipro UGENE to version 1.16.2.
23 Mar 2015 01:44:44
Original commit files touched by this commit Revision:381974  1.16.1
danfe search for other commits by this committer
- Update to version 1.16.1
- Explicitly list all required Qt components in USE_QT4 instead of relying
  on them being silently picked up through `www/webkit-qt4' dependency
- Group *_build components together while here
- Remove one REINPLACE_CMD call that is no longer needed
24 Feb 2015 11:42:54
Original commit files touched by this commit Revision:379787  1.16.0
danfe search for other commits by this committer
Update Unipro UGENE to version 1.16.0 (documentation was also rerolled).
06 Jan 2015 05:28:59
Original commit files touched by this commit Revision:376383  1.15.1
danfe search for other commits by this committer
Update to version 1.15.1.
03 Dec 2014 01:40:55
Original commit files touched by this commit Revision:373799  1.15.0
danfe search for other commits by this committer
Update to version 1.15.0.
20 Oct 2014 07:10:48
Original commit files touched by this commit Revision:371237  1.14.2
bapt search for other commits by this committer
Cleanup plist
13 Oct 2014 11:01:52
Original commit files touched by this commit Revision:370764  1.14.2
danfe search for other commits by this committer
Update to version 1.14.2.
10 Sep 2014 20:50:37
Original commit files touched by this commit Revision:367888  1.14.0_1
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)
01 Sep 2014 07:39:00
Original commit files touched by this commit Revision:366842  1.14.0
danfe search for other commits by this committer
- Update Unipro UGENE and documentation to version 1.14.0
- Remove patches integrated upstream (it's nice to have direct contact)
- Sort USES and pkg-plist, cleanup Makefile a bit while here

Approved by:	maintainer (implicit)
04 Aug 2014 23:06:21
Original commit files touched by this commit Revision:364067  1.13.1
bapt search for other commits by this committer
USES=execinfo
07 Mar 2014 07:39:21
Original commit files touched by this commit Revision:347340  1.13.1
danfe search for other commits by this committer
Update to version 1.13.1.
30 Jan 2014 13:38:26
Original commit files touched by this commit Revision:341837  1.13.0
danfe search for other commits by this committer
Unbreak the fetch: one of the documentation PDF files was rerolled.
30 Jan 2014 13:11:41
Original commit files touched by this commit Revision:341835  1.13.0
decke search for other commits by this committer
- Mark BROKEN because it does not fetch
16 Jan 2014 17:17:16
Original commit files touched by this commit Revision:339938  1.13.0
danfe search for other commits by this committer
- Update to version 1.13.0 and improve FreeBSD support; it also builds
  pretty cleanly with GCC v4.2, v4.6, and Clang (modulo a few warnings)
- Sadly, do not use PORTDOCS: since DOCSDIR is set to be inside DATADIR,
  and will get appended to PLIST after @dirrm %%DATADIR%%, which upsets
  sanity checking tools; instead, list the docs explicitly in DISTFILES
  and add them to pkg-plist (guarded by %%PORTDOCS%%)

Tested on:	i386 (only)
01 Nov 2013 15:20:29
Original commit files touched by this commit Revision:332391  1.12.3
danfe search for other commits by this committer
- Install official UGENE documentation (PDF)
- Utilize DIST_SUBDIR as now it's more than one distfile
31 Oct 2013 15:30:04
Original commit files touched by this commit Revision:332256  1.12.3
danfe search for other commits by this committer
- Update to version 1.12.3
- Conditionalize dependency on `devel/libexecinfo'
- Try to detect SSE2 support
- Convert to USES=qmake and stafigy
- Improve grammar in port description while here

Approved by:	maintainer (implicit)
22 Oct 2013 13:57:35
Original commit files touched by this commit Revision:331271  1.11.4
amdmi3 search for other commits by this committer
- Remove manual creation and removal of share/applications, as it's now in the
mtree (categories starting with [bce])

Approved by:	portmgr (bdrewery)
20 Sep 2013 15:55:44
Original commit files touched by this commit Revision:327709  1.11.4
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
14 Aug 2013 22:35:54
Original commit files touched by this commit Revision:324744  1.11.4  Sanity Test Failure
ak search for other commits by this committer
- Remove MAKE_JOBS_SAFE variable

Approved by:	portmgr (bdrewery)
25 Feb 2013 13:00:16
Original commit files touched by this commit Revision:312918  1.11.4
danfe search for other commits by this committer
Unbreak on 7.X and i386 systems.

Reported by:	QAT
23 Feb 2013 04:50:48
Original commit files touched by this commit Revision:312798  1.11.4
danfe search for other commits by this committer
Add Unipro UGENE, a free open-source crowss-platform bioinformatics software.

PR:		ports/173387
Submitted by:	Hannes Hauswedell

Number of commits found: 53