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Port details
ugene Integrated bioinformatics toolkit
40.1_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 40.1Version 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: 2024-01-10 08:16:01
Commit Hash: 1b819e4
Also Listed In: science
License: GPLv2+
WWW:
https://ugene.net/
Description:
Unipro UGENE is multiplatform, open-source software with the main goal of assisting molecular biologists without much expertise in bioinformatics to manage, analyze, and visualize their data. UGENE integrates widely used bioinformatics tools within one common user interface. UGENE toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees, and 3D structures.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (1324 items)
Collapse this list.
  1. /usr/local/share/licenses/ugene-40.1_1/catalog.mk
  2. /usr/local/share/licenses/ugene-40.1_1/LICENSE
  3. /usr/local/share/licenses/ugene-40.1_1/GPLv2+
  4. bin/ugene
  5. lib/ugene/libQSpec.so
  6. lib/ugene/libU2Algorithm.so
  7. lib/ugene/libU2Core.so
  8. lib/ugene/libU2Designer.so
  9. lib/ugene/libU2Formats.so
  10. lib/ugene/libU2Gui.so
  11. lib/ugene/libU2Lang.so
  12. lib/ugene/libU2Private.so
  13. lib/ugene/libU2Script.so
  14. lib/ugene/libU2Test.so
  15. lib/ugene/libU2View.so
  16. lib/ugene/plugins/CoreTests.license
  17. lib/ugene/plugins/CoreTests.plugin
  18. lib/ugene/plugins/GUITestBase.license
  19. lib/ugene/plugins/GUITestBase.plugin
  20. lib/ugene/plugins/annotator.license
  21. lib/ugene/plugins/annotator.plugin
  22. lib/ugene/plugins/api_tests.license
  23. lib/ugene/plugins/api_tests.plugin
  24. lib/ugene/plugins/ball.license
  25. lib/ugene/plugins/ball.plugin
  26. lib/ugene/plugins/biostruct3d_view.license
  27. lib/ugene/plugins/biostruct3d_view.plugin
  28. lib/ugene/plugins/chroma_view.license
  29. lib/ugene/plugins/chroma_view.plugin
  30. lib/ugene/plugins/circular_view.license
  31. lib/ugene/plugins/circular_view.plugin
  32. lib/ugene/plugins/clark_support.license
  33. lib/ugene/plugins/clark_support.plugin
  34. lib/ugene/plugins/dbi_bam.license
  35. lib/ugene/plugins/dbi_bam.plugin
  36. lib/ugene/plugins/diamond_support.license
  37. lib/ugene/plugins/diamond_support.plugin
  38. lib/ugene/plugins/dna_export.license
  39. lib/ugene/plugins/dna_export.plugin
  40. lib/ugene/plugins/dna_flexibility.license
  41. lib/ugene/plugins/dna_flexibility.plugin
  42. lib/ugene/plugins/dna_graphpack.license
  43. lib/ugene/plugins/dna_graphpack.plugin
  44. lib/ugene/plugins/dna_stat.license
  45. lib/ugene/plugins/dna_stat.plugin
  46. lib/ugene/plugins/dotplot.license
  47. lib/ugene/plugins/dotplot.plugin
  48. lib/ugene/plugins/enzymes.license
  49. lib/ugene/plugins/enzymes.plugin
  50. lib/ugene/plugins/external_tool_support.license
  51. lib/ugene/plugins/external_tool_support.plugin
  52. lib/ugene/plugins/genome_aligner.license
  53. lib/ugene/plugins/genome_aligner.plugin
  54. lib/ugene/plugins/gor4.license
  55. lib/ugene/plugins/gor4.plugin
  56. lib/ugene/plugins/hmm2.license
  57. lib/ugene/plugins/hmm2.plugin
  58. lib/ugene/plugins/kalign.license
  59. lib/ugene/plugins/kalign.plugin
  60. lib/ugene/plugins/kraken_support.license
  61. lib/ugene/plugins/kraken_support.plugin
  62. lib/ugene/plugins/libCoreTests.so
  63. lib/ugene/plugins/libGUITestBase.so
  64. lib/ugene/plugins/libannotator.so
  65. lib/ugene/plugins/libapi_tests.so
  66. lib/ugene/plugins/libball.so
  67. lib/ugene/plugins/libbiostruct3d_view.so
  68. lib/ugene/plugins/libchroma_view.so
  69. lib/ugene/plugins/libcircular_view.so
  70. lib/ugene/plugins/libclark_support.so
  71. lib/ugene/plugins/libdbi_bam.so
  72. lib/ugene/plugins/libdiamond_support.so
  73. lib/ugene/plugins/libdna_export.so
  74. lib/ugene/plugins/libdna_flexibility.so
  75. lib/ugene/plugins/libdna_graphpack.so
  76. lib/ugene/plugins/libdna_stat.so
  77. lib/ugene/plugins/libdotplot.so
  78. lib/ugene/plugins/libenzymes.so
  79. lib/ugene/plugins/libexternal_tool_support.so
  80. lib/ugene/plugins/libgenome_aligner.so
  81. lib/ugene/plugins/libgor4.so
  82. lib/ugene/plugins/libhmm2.so
  83. lib/ugene/plugins/libkalign.so
  84. lib/ugene/plugins/libkraken_support.so
  85. lib/ugene/plugins/liblinkdata_support.so
  86. lib/ugene/plugins/libmetaphlan2_support.so
  87. lib/ugene/plugins/libngs_reads_classification.so
  88. lib/ugene/plugins/libopencl_support.so
  89. lib/ugene/plugins/liborf_marker.so
  90. lib/ugene/plugins/libpcr.so
  91. lib/ugene/plugins/libperf_monitor.so
  92. lib/ugene/plugins/libphylip.so
  93. lib/ugene/plugins/libprimer3.so
  94. lib/ugene/plugins/libpsipred.so
  95. lib/ugene/plugins/libptools.so
  96. lib/ugene/plugins/libquery_designer.so
  97. lib/ugene/plugins/libremote_blast.so
  98. lib/ugene/plugins/librepeat_finder.so
  99. lib/ugene/plugins/libsitecon.so
  100. lib/ugene/plugins/libsmith_waterman.so
  101. lib/ugene/plugins/libtest_runner.so
  102. lib/ugene/plugins/libumuscle.so
  103. lib/ugene/plugins/libvariants.so
  104. lib/ugene/plugins/libweight_matrix.so
  105. lib/ugene/plugins/libwevote_support.so
  106. lib/ugene/plugins/libworkflow_designer.so
  107. lib/ugene/plugins/linkdata_support.license
  108. lib/ugene/plugins/linkdata_support.plugin
  109. lib/ugene/plugins/metaphlan2_support.license
  110. lib/ugene/plugins/metaphlan2_support.plugin
  111. lib/ugene/plugins/ngs_reads_classification.license
  112. lib/ugene/plugins/ngs_reads_classification.plugin
  113. lib/ugene/plugins/opencl_support.license
  114. lib/ugene/plugins/opencl_support.plugin
  115. lib/ugene/plugins/orf_marker.license
  116. lib/ugene/plugins/orf_marker.plugin
  117. lib/ugene/plugins/pcr.license
  118. lib/ugene/plugins/pcr.plugin
  119. lib/ugene/plugins/perf_monitor.license
  120. lib/ugene/plugins/perf_monitor.plugin
  121. lib/ugene/plugins/phylip.license
  122. lib/ugene/plugins/phylip.plugin
  123. lib/ugene/plugins/primer3.license
  124. lib/ugene/plugins/primer3.plugin
  125. lib/ugene/plugins/psipred.license
  126. lib/ugene/plugins/psipred.plugin
  127. lib/ugene/plugins/ptools.license
  128. lib/ugene/plugins/ptools.plugin
  129. lib/ugene/plugins/query_designer.license
  130. lib/ugene/plugins/query_designer.plugin
  131. lib/ugene/plugins/remote_blast.license
  132. lib/ugene/plugins/remote_blast.plugin
  133. lib/ugene/plugins/repeat_finder.license
  134. lib/ugene/plugins/repeat_finder.plugin
  135. lib/ugene/plugins/sitecon.license
  136. lib/ugene/plugins/sitecon.plugin
  137. lib/ugene/plugins/smith_waterman.license
  138. lib/ugene/plugins/smith_waterman.plugin
  139. lib/ugene/plugins/test_runner.license
  140. lib/ugene/plugins/test_runner.plugin
  141. lib/ugene/plugins/umuscle.license
  142. lib/ugene/plugins/umuscle.plugin
  143. lib/ugene/plugins/variants.license
  144. lib/ugene/plugins/variants.plugin
  145. lib/ugene/plugins/weight_matrix.license
  146. lib/ugene/plugins/weight_matrix.plugin
  147. lib/ugene/plugins/wevote_support.license
  148. lib/ugene/plugins/wevote_support.plugin
  149. lib/ugene/plugins/workflow_designer.license
  150. lib/ugene/plugins/workflow_designer.plugin
  151. lib/ugene/plugins_checker
  152. lib/ugene/transl_ru.qm
  153. lib/ugene/transl_tr.qm
  154. lib/ugene/ugene
  155. lib/ugene/ugenecl
  156. lib/ugene/ugenem
  157. lib/ugene/ugeneui
  158. share/man/man1/ugene.1.gz
  159. share/applications/ugene.desktop
  160. share/icons/hicolor/32x32/mimetypes/application-x-ugene-ext.png
  161. share/mime/packages/application-x-ugene.xml
  162. share/pixmaps/ugene.png
  163. share/pixmaps/ugene.xpm
  164. share/ugene/DBXRefRegistry.txt
  165. share/ugene/adapters/adapters.fasta
  166. share/ugene/adapters/illumina/NexteraPE-PE.fa
  167. share/ugene/adapters/illumina/TruSeq2-PE.fa
  168. share/ugene/adapters/illumina/TruSeq2-SE.fa
  169. share/ugene/adapters/illumina/TruSeq3-PE-2.fa
  170. share/ugene/adapters/illumina/TruSeq3-PE.fa
  171. share/ugene/adapters/illumina/TruSeq3-SE.fa
  172. share/ugene/back_translation/Bacteria/Arthrobacter_aurescens_TC1.cut
  173. share/ugene/back_translation/Bacteria/Bacillus_subtilis.cut
  174. share/ugene/back_translation/Bacteria/Escherichia_coli.cut
  175. share/ugene/back_translation/Bacteria/Haemophilus_influenzae.cut
  176. share/ugene/back_translation/Bacteria/Helicobacter_pylori.cut
  177. share/ugene/back_translation/Bacteria/Listeria_monocytogenes.cut
  178. share/ugene/back_translation/Bacteria/Neisseria_meningitidis.cut
  179. share/ugene/back_translation/Bacteria/Salmonella_typhimurium_LT2.cut
  180. share/ugene/back_translation/Bacteria/Streptomyces_coelicolor_A3(2).cut
  181. share/ugene/back_translation/Bacteria/Sulfolobus_solfataricus_P2.cut
  182. share/ugene/back_translation/Invertebrates/Apis_mellifera_(honey_bee).cut
  183. share/ugene/back_translation/Invertebrates/Caenorhabditis_elegans.cut
  184. share/ugene/back_translation/Invertebrates/Drosophila_melanogaster_(fruit_fly).cut
  185. share/ugene/back_translation/Invertebrates/Plasmodium_falciparum_(malaria_parasite_P._falciparum).cut
  186. share/ugene/back_translation/Invertebrates/mitochondrion_Caenorhabditis_elegans.cut
  187. share/ugene/back_translation/Invertebrates/mitochondrion_Drosophila_melanogaster_(fruit_fly).cut
  188. share/ugene/back_translation/Mammalia/Bos_taurus_(cow).cut
  189. share/ugene/back_translation/Mammalia/Canis_familiaris_(dog).cut
  190. share/ugene/back_translation/Mammalia/Sus_scrofa_(pig).cut
  191. share/ugene/back_translation/Mammalia/mitochondrion_Bos_taurus_(cow).cut
  192. share/ugene/back_translation/Mammalia/mitochondrion_Sus_scrofa_(pig).cut
  193. share/ugene/back_translation/Plants/Arabidopsis_thaliana_(thale_cress).cut
  194. share/ugene/back_translation/Plants/Oryza_sativa.cut
  195. share/ugene/back_translation/Plants/Zea_mays.cut
  196. share/ugene/back_translation/Primates/Homo_sapiens_(human).cut
  197. share/ugene/back_translation/Primates/Pan_troglodytes_(chimpanzee).cut
  198. share/ugene/back_translation/Primates/mitochondrion_Homo_sapiens_(human).cut
  199. share/ugene/back_translation/Primates/mitochondrion_Pan_troglodytes_(chimpanzee).cut
  200. share/ugene/back_translation/Rodents/Mus_musculus_(house_mouse).cut
  201. share/ugene/back_translation/Rodents/Rattus_norvegicus_(Norway_rat).cut
  202. share/ugene/back_translation/Vertebrates/Gallus_gallus_(chicken).cut
  203. share/ugene/back_translation/Vertebrates/Takifugu_rubripes_(Fugu_rubripes).cut
  204. share/ugene/back_translation/Vertebrates/Xenopus_laevis_(African_clawed_frog).cut
  205. share/ugene/back_translation/Vertebrates/mitochondrion_Gallus_gallus_(chicken).cut
  206. share/ugene/back_translation/Vertebrates/mitochondrion_Takifugu_rubripes_(Fugu_rubripes).cut
  207. share/ugene/back_translation/Viruses/Human_immunodeficiency_virus_1_(HIV-1).cut
  208. share/ugene/back_translation/Viruses/Influenza_A_virus.cut
  209. share/ugene/back_translation/Yeast/Saccharomyces_cerevisiae_(baker's_yeast).cut
  210. share/ugene/back_translation/tables.xml
  211. share/ugene/biostruct3d_plugin/BioStruct3DLinks.txt
  212. share/ugene/cmdline/align-clustalo.uwl
  213. share/ugene/cmdline/align-clustalw.uwl
  214. share/ugene/cmdline/align-kalign.uwl
  215. share/ugene/cmdline/align-mafft.uwl
  216. share/ugene/cmdline/align-tcoffee.uwl
  217. share/ugene/cmdline/align-to-reference.uwl
  218. share/ugene/cmdline/align.uwl
  219. share/ugene/cmdline/convert-msa.uwl
  220. share/ugene/cmdline/convert-seq.uwl
  221. share/ugene/cmdline/extract-sequence.uwl
  222. share/ugene/cmdline/extract_consensus_sequence.uwl
  223. share/ugene/cmdline/extract_consensus_string.uwl
  224. share/ugene/cmdline/extract_coverage.uwl
  225. share/ugene/cmdline/fetch-sequence.uwl
  226. share/ugene/cmdline/find-orfs.uwl
  227. share/ugene/cmdline/find-repeats.uwl
  228. share/ugene/cmdline/find-sw.uwl
  229. share/ugene/cmdline/gene-by-gene.uwl
  230. share/ugene/cmdline/generate-dna.uwl
  231. share/ugene/cmdline/hmm2-build.uwl
  232. share/ugene/cmdline/hmm2-search.uwl
  233. share/ugene/cmdline/hmm3-build-and-search.uwl
  234. share/ugene/cmdline/hmm3-search.uwl
  235. share/ugene/cmdline/join-quality.uwl
  236. share/ugene/cmdline/local-blast+.uwl
  237. share/ugene/cmdline/pfm-build.uwl
  238. share/ugene/cmdline/pfm-search.uwl
  239. share/ugene/cmdline/pwm-build.uwl
  240. share/ugene/cmdline/pwm-search.uwl
  241. share/ugene/cmdline/query.uwl
  242. share/ugene/cmdline/remote-request.uwl
  243. share/ugene/cmdline/revcompl.uwl
  244. share/ugene/cmdline/sitecon-build.uwl
  245. share/ugene/cmdline/sitecon-search.uwl
  246. share/ugene/cmdline/snp.uwl
  247. share/ugene/custom_annotations/plasmid_features.txt
  248. share/ugene/enzymes/2013_08_01.bairoch.gz
  249. share/ugene/genome_lengths/danRer7.genome
  250. share/ugene/genome_lengths/ecoli.genome
  251. share/ugene/genome_lengths/hg18.genome
  252. share/ugene/genome_lengths/hg19.genome
  253. share/ugene/genome_lengths/mm10.genome
  254. share/ugene/genome_lengths/mm8.genome
  255. share/ugene/genome_lengths/mm9.genome
  256. share/ugene/genome_lengths/test.genome
  257. share/ugene/license
  258. share/ugene/position_weight_matrix/JASPAR/all_jaspar.csv
  259. share/ugene/position_weight_matrix/JASPAR/fungi/MA0265.1.pfm
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  724. share/ugene/position_weight_matrix/UniPROBE/Cell08/Alx3_3418.2.pwm
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  726. share/ugene/position_weight_matrix/UniPROBE/Cell08/Arx_1738.2.pwm
  727. share/ugene/position_weight_matrix/UniPROBE/Cell08/Bapx1_2343.1.pwm
  728. share/ugene/position_weight_matrix/UniPROBE/Cell08/Barhl1_2590.2.pwm
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  731. share/ugene/position_weight_matrix/UniPROBE/Cell08/Barx2_3447.2.pwm
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  733. share/ugene/position_weight_matrix/UniPROBE/Cell08/Cart1_0997.1.pwm
  734. share/ugene/position_weight_matrix/UniPROBE/Cell08/Cart1_1275.1.pwm
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  736. share/ugene/position_weight_matrix/UniPROBE/Cell08/Cdx2_4272.1.pwm
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  738. share/ugene/position_weight_matrix/UniPROBE/Cell08/Crx_3485.1.pwm
  739. share/ugene/position_weight_matrix/UniPROBE/Cell08/Cutl1_3494.1.pwm
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  741. share/ugene/position_weight_matrix/UniPROBE/Cell08/Dbx1_3486.1.pwm
  742. share/ugene/position_weight_matrix/UniPROBE/Cell08/Dbx2_3487.1.pwm
  743. share/ugene/position_weight_matrix/UniPROBE/Cell08/Dlx1_1741.2.pwm
  744. share/ugene/position_weight_matrix/UniPROBE/Cell08/Dlx2_2273.2.pwm
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  746. share/ugene/position_weight_matrix/UniPROBE/Cell08/Dlx4_3488.2.pwm
  747. share/ugene/position_weight_matrix/UniPROBE/Cell08/Dlx5_3419.2.pwm
  748. share/ugene/position_weight_matrix/UniPROBE/Cell08/Dmbx1_2277.1.pwm
  749. share/ugene/position_weight_matrix/UniPROBE/Cell08/Dobox4_3956.2.pwm
  750. share/ugene/position_weight_matrix/UniPROBE/Cell08/Dobox5_3493.1.pwm
  751. share/ugene/position_weight_matrix/UniPROBE/Cell08/Duxl_1286.2.pwm
  752. share/ugene/position_weight_matrix/UniPROBE/Cell08/Emx2_3420.1.pwm
  753. share/ugene/position_weight_matrix/UniPROBE/Cell08/En1_3123.2.pwm
  754. share/ugene/position_weight_matrix/UniPROBE/Cell08/En2_0952.1.pwm
  755. share/ugene/position_weight_matrix/UniPROBE/Cell08/Esx1_3124.2.pwm
  756. share/ugene/position_weight_matrix/UniPROBE/Cell08/Evx1_3952.2.pwm
  757. share/ugene/position_weight_matrix/UniPROBE/Cell08/Evx2_2645.3.pwm
  758. share/ugene/position_weight_matrix/UniPROBE/Cell08/Gbx1_2883.2.pwm
  759. share/ugene/position_weight_matrix/UniPROBE/Cell08/Gbx2_3110.1.pwm
  760. share/ugene/position_weight_matrix/UniPROBE/Cell08/Gsc_2327.3.pwm
  761. share/ugene/position_weight_matrix/UniPROBE/Cell08/Gsh2_3990.2.pwm
  762. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hdx_3845.3.pwm
  763. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hlx1_2350.1.pwm
  764. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hlxb9_3422.1.pwm
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  766. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hmx1_3423.1.pwm
  767. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hmx2_3424.3.pwm
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  769. share/ugene/position_weight_matrix/UniPROBE/Cell08/Homez_1063.2.pwm
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  771. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxa11_2218.1.pwm
  772. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxa13_3126.1.pwm
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  774. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxa2_3079.1.pwm
  775. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxa3_2783.2.pwm
  776. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxa4_3426.1.pwm
  777. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxa5_3415.1.pwm
  778. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxa6_1040.1.pwm
  779. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxa7_2668.2.pwm
  780. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxa7_3750.1.pwm
  781. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxa9_2622.2.pwm
  782. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxb13_3479.1.pwm
  783. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxb3_1720.2.pwm
  784. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxb4_2627.1.pwm
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  786. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxb6_3428.2.pwm
  787. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxb7_3953.1.pwm
  788. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxb8_3780.2.pwm
  789. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxb9_3413.1.pwm
  790. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxc10_2779.2.pwm
  791. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxc11_3718.2.pwm
  792. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxc12_3480.1.pwm
  793. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxc13_3127.1.pwm
  794. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxc4_3491.1.pwm
  795. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxc5_2630.2.pwm
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  799. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxd10_2368.2.pwm
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  802. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxd13_2356.1.pwm
  803. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxd1_3448.1.pwm
  804. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxd3_1742.2.pwm
  805. share/ugene/position_weight_matrix/UniPROBE/Cell08/Hoxd8_2644.1.pwm
  806. share/ugene/position_weight_matrix/UniPROBE/Cell08/Ipf1_3815.1.pwm
  807. share/ugene/position_weight_matrix/UniPROBE/Cell08/Irx2_0900.3.pwm
  808. share/ugene/position_weight_matrix/UniPROBE/Cell08/Irx3_0920.1.pwm
  809. share/ugene/position_weight_matrix/UniPROBE/Cell08/Irx3_2226.1.pwm
  810. share/ugene/position_weight_matrix/UniPROBE/Cell08/Irx4_2242.3.pwm
  811. share/ugene/position_weight_matrix/UniPROBE/Cell08/Irx5_2385.1.pwm
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  813. share/ugene/position_weight_matrix/UniPROBE/Cell08/Isl2_3430.1.pwm
  814. share/ugene/position_weight_matrix/UniPROBE/Cell08/Isx_3445.1.pwm
  815. share/ugene/position_weight_matrix/UniPROBE/Cell08/Lbx2_3869.2.pwm
  816. share/ugene/position_weight_matrix/UniPROBE/Cell08/Lhx1_2240.2.pwm
  817. share/ugene/position_weight_matrix/UniPROBE/Cell08/Lhx2_0953.2.pwm
  818. share/ugene/position_weight_matrix/UniPROBE/Cell08/Lhx3_3431.1.pwm
  819. share/ugene/position_weight_matrix/UniPROBE/Cell08/Lhx4_1719.2.pwm
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  821. share/ugene/position_weight_matrix/UniPROBE/Cell08/Lhx6_2272.1.pwm
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  824. share/ugene/position_weight_matrix/UniPROBE/Cell08/Lhx9_3492.1.pwm
  825. share/ugene/position_weight_matrix/UniPROBE/Cell08/Lmx1a_2238.2.pwm
  826. share/ugene/position_weight_matrix/UniPROBE/Cell08/Lmx1b_3433.2.pwm
  827. share/ugene/position_weight_matrix/UniPROBE/Cell08/Meis1_2335.1.pwm
  828. share/ugene/position_weight_matrix/UniPROBE/Cell08/Meox1_2310.2.pwm
  829. share/ugene/position_weight_matrix/UniPROBE/Cell08/Mrg1_2246.2.pwm
  830. share/ugene/position_weight_matrix/UniPROBE/Cell08/Mrg2_2302.1.pwm
  831. share/ugene/position_weight_matrix/UniPROBE/Cell08/Msx1_3031.2.pwm
  832. share/ugene/position_weight_matrix/UniPROBE/Cell08/Msx2_3449.1.pwm
  833. share/ugene/position_weight_matrix/UniPROBE/Cell08/Msx3_3206.1.pwm
  834. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx1-1_3856.3.pwm
  835. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx1-2_3214.1.pwm
  836. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx2-2_2823.1.pwm
  837. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx2-3_3435.1.pwm
  838. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx2-4_3074.1.pwm
  839. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx2-5_3436.1.pwm
  840. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx2-6_3437.1.pwm
  841. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx2-9_3082.1.pwm
  842. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx3-1_2923.2.pwm
  843. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx6-1_2825.1.pwm
  844. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx6-1_2825.2.pwm
  845. share/ugene/position_weight_matrix/UniPROBE/Cell08/Nkx6-3_3446.1.pwm
  846. share/ugene/position_weight_matrix/UniPROBE/Cell08/Obox1_3970.2.pwm
  847. share/ugene/position_weight_matrix/UniPROBE/Cell08/Obox2_3438.2.pwm
  848. share/ugene/position_weight_matrix/UniPROBE/Cell08/Obox3_3439.1.pwm
  849. share/ugene/position_weight_matrix/UniPROBE/Cell08/Obox5_2284.1.pwm
  850. share/ugene/position_weight_matrix/UniPROBE/Cell08/Obox5_3963.2.pwm
  851. share/ugene/position_weight_matrix/UniPROBE/Cell08/Obox6_3440.2.pwm
  852. share/ugene/position_weight_matrix/UniPROBE/Cell08/Og2x_3719.1.pwm
  853. share/ugene/position_weight_matrix/UniPROBE/Cell08/Otp_3496.1.pwm
  854. share/ugene/position_weight_matrix/UniPROBE/Cell08/Otx1_2325.1.pwm
  855. share/ugene/position_weight_matrix/UniPROBE/Cell08/Otx2_3441.1.pwm
  856. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pax4_3989.2.pwm
  857. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pax6_3838.3.pwm
  858. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pax7_3783.1.pwm
  859. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pbx1_3203.1.pwm
  860. share/ugene/position_weight_matrix/UniPROBE/Cell08/Phox2a_3947.1.pwm
  861. share/ugene/position_weight_matrix/UniPROBE/Cell08/Phox2b_3948.1.pwm
  862. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pitx1_2312.1.pwm
  863. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pitx2_2274.3.pwm
  864. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pitx3_3497.2.pwm
  865. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pknox1_2364.2.pwm
  866. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pknox2_3077.2.pwm
  867. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou1f1_3818.1.pwm
  868. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou2f1_3081.2.pwm
  869. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou2f2_3748.1.pwm
  870. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou2f3_3986.2.pwm
  871. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou3f1_3819.1.pwm
  872. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou3f2_2824.1.pwm
  873. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou3f3_3235.2.pwm
  874. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou3f4_3773.1.pwm
  875. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou4f3_2791.1.pwm
  876. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou6f1_1731.2.pwm
  877. share/ugene/position_weight_matrix/UniPROBE/Cell08/Pou6f1_3733.1.pwm
  878. share/ugene/position_weight_matrix/UniPROBE/Cell08/Prop1_3949.1.pwm
  879. share/ugene/position_weight_matrix/UniPROBE/Cell08/Prrx1_3442.1.pwm
  880. share/ugene/position_weight_matrix/UniPROBE/Cell08/Prrx2_3072.1.pwm
  881. share/ugene/position_weight_matrix/UniPROBE/Cell08/Rax_3443.1.pwm
  882. share/ugene/position_weight_matrix/UniPROBE/Cell08/Rhox11_1765.2.pwm
  883. share/ugene/position_weight_matrix/UniPROBE/Cell08/Rhox11_2205.1.pwm
  884. share/ugene/position_weight_matrix/UniPROBE/Cell08/Rhox6_4251.1.pwm
  885. share/ugene/position_weight_matrix/UniPROBE/Cell08/Shox2_2641.2.pwm
  886. share/ugene/position_weight_matrix/UniPROBE/Cell08/Six1_0935.2.pwm
  887. share/ugene/position_weight_matrix/UniPROBE/Cell08/Six2_2307.2.pwm
  888. share/ugene/position_weight_matrix/UniPROBE/Cell08/Six3_1732.2.pwm
  889. share/ugene/position_weight_matrix/UniPROBE/Cell08/Six4_2860.1.pwm
  890. share/ugene/position_weight_matrix/UniPROBE/Cell08/Six6_2267.4.pwm
  891. share/ugene/position_weight_matrix/UniPROBE/Cell08/Six6_2267.5.pwm
  892. share/ugene/position_weight_matrix/UniPROBE/Cell08/Tcf1_2666.2.pwm
  893. share/ugene/position_weight_matrix/UniPROBE/Cell08/Tcf2_0913.2.pwm
  894. share/ugene/position_weight_matrix/UniPROBE/Cell08/Tgif1_2342.2.pwm
  895. share/ugene/position_weight_matrix/UniPROBE/Cell08/Tgif2_3451.1.pwm
  896. share/ugene/position_weight_matrix/UniPROBE/Cell08/Titf1_1722.2.pwm
  897. share/ugene/position_weight_matrix/UniPROBE/Cell08/Tlx2_3498.2.pwm
  898. share/ugene/position_weight_matrix/UniPROBE/Cell08/Uncx4.1_2281.2.pwm
  899. share/ugene/position_weight_matrix/UniPROBE/Cell08/Vax1_3499.1.pwm
  900. share/ugene/position_weight_matrix/UniPROBE/Cell08/Vax2_3500.1.pwm
  901. share/ugene/position_weight_matrix/UniPROBE/Cell08/Vsx1_1728.1.pwm
  902. share/ugene/position_weight_matrix/UniPROBE/GR09/Aft1.pwm
  903. share/ugene/position_weight_matrix/UniPROBE/GR09/Aro80.pwm
  904. share/ugene/position_weight_matrix/UniPROBE/GR09/Asg1.pwm
  905. share/ugene/position_weight_matrix/UniPROBE/GR09/Bas1.pwm
  906. share/ugene/position_weight_matrix/UniPROBE/GR09/Cbf1.pwm
  907. share/ugene/position_weight_matrix/UniPROBE/GR09/Cep3.pwm
  908. share/ugene/position_weight_matrix/UniPROBE/GR09/Cha4.pwm
  909. share/ugene/position_weight_matrix/UniPROBE/GR09/Cup9.pwm
  910. share/ugene/position_weight_matrix/UniPROBE/GR09/Ecm22.pwm
  911. share/ugene/position_weight_matrix/UniPROBE/GR09/Fhl1.pwm
  912. share/ugene/position_weight_matrix/UniPROBE/GR09/Fkh1.pwm
  913. share/ugene/position_weight_matrix/UniPROBE/GR09/Fkh2.pwm
  914. share/ugene/position_weight_matrix/UniPROBE/GR09/Gal4.pwm
  915. share/ugene/position_weight_matrix/UniPROBE/GR09/Gat1.pwm
  916. share/ugene/position_weight_matrix/UniPROBE/GR09/Gat3.pwm
  917. share/ugene/position_weight_matrix/UniPROBE/GR09/Gat4.pwm
  918. share/ugene/position_weight_matrix/UniPROBE/GR09/Gcn4.pwm
  919. share/ugene/position_weight_matrix/UniPROBE/GR09/Gln3.pwm
  920. share/ugene/position_weight_matrix/UniPROBE/GR09/Gsm1.pwm
  921. share/ugene/position_weight_matrix/UniPROBE/GR09/Gzf3.pwm
  922. share/ugene/position_weight_matrix/UniPROBE/GR09/Hal9.pwm
  923. share/ugene/position_weight_matrix/UniPROBE/GR09/Leu3.pwm
  924. share/ugene/position_weight_matrix/UniPROBE/GR09/Lys14.pwm
  925. share/ugene/position_weight_matrix/UniPROBE/GR09/Matalpha2.pwm
  926. share/ugene/position_weight_matrix/UniPROBE/GR09/Mbp1.pwm
  927. share/ugene/position_weight_matrix/UniPROBE/GR09/Mcm1.pwm
  928. share/ugene/position_weight_matrix/UniPROBE/GR09/Met32.pwm
  929. share/ugene/position_weight_matrix/UniPROBE/GR09/Mga1.pwm
  930. share/ugene/position_weight_matrix/UniPROBE/GR09/Mig1.pwm
  931. share/ugene/position_weight_matrix/UniPROBE/GR09/Mig2.pwm
  932. share/ugene/position_weight_matrix/UniPROBE/GR09/Mig3.pwm
  933. share/ugene/position_weight_matrix/UniPROBE/GR09/Ndt80.pwm
  934. share/ugene/position_weight_matrix/UniPROBE/GR09/Nhp6a.pwm
  935. share/ugene/position_weight_matrix/UniPROBE/GR09/Nhp6b.pwm
  936. share/ugene/position_weight_matrix/UniPROBE/GR09/Nrg1.pwm
  937. share/ugene/position_weight_matrix/UniPROBE/GR09/Oaf1.pwm
  938. share/ugene/position_weight_matrix/UniPROBE/GR09/Pbf1.pwm
  939. share/ugene/position_weight_matrix/UniPROBE/GR09/Pbf2.pwm
  940. share/ugene/position_weight_matrix/UniPROBE/GR09/Pdr1.pwm
  941. share/ugene/position_weight_matrix/UniPROBE/GR09/Phd1.pwm
  942. share/ugene/position_weight_matrix/UniPROBE/GR09/Pho2.pwm
  943. share/ugene/position_weight_matrix/UniPROBE/GR09/Pho4.pwm
  944. share/ugene/position_weight_matrix/UniPROBE/GR09/Put3.pwm
  945. share/ugene/position_weight_matrix/UniPROBE/GR09/Rap1.pwm
  946. share/ugene/position_weight_matrix/UniPROBE/GR09/Rdr1.pwm
  947. share/ugene/position_weight_matrix/UniPROBE/GR09/Rds1.pwm
  948. share/ugene/position_weight_matrix/UniPROBE/GR09/Rds2.pwm
  949. share/ugene/position_weight_matrix/UniPROBE/GR09/Rgt1.pwm
  950. share/ugene/position_weight_matrix/UniPROBE/GR09/Rph1.pwm
  951. share/ugene/position_weight_matrix/UniPROBE/GR09/Rpn4.pwm
  952. share/ugene/position_weight_matrix/UniPROBE/GR09/Rsc3.pwm
  953. share/ugene/position_weight_matrix/UniPROBE/GR09/Rsc30.pwm
  954. share/ugene/position_weight_matrix/UniPROBE/GR09/Rtg3.pwm
  955. share/ugene/position_weight_matrix/UniPROBE/GR09/Sfl1.pwm
  956. share/ugene/position_weight_matrix/UniPROBE/GR09/Sfp1.pwm
  957. share/ugene/position_weight_matrix/UniPROBE/GR09/Sip4.pwm
  958. share/ugene/position_weight_matrix/UniPROBE/GR09/Skn7.pwm
  959. share/ugene/position_weight_matrix/UniPROBE/GR09/Smp1.pwm
  960. share/ugene/position_weight_matrix/UniPROBE/GR09/Spt15.pwm
  961. share/ugene/position_weight_matrix/UniPROBE/GR09/Srd1.pwm
  962. share/ugene/position_weight_matrix/UniPROBE/GR09/Stb3.pwm
  963. share/ugene/position_weight_matrix/UniPROBE/GR09/Stp2.pwm
  964. share/ugene/position_weight_matrix/UniPROBE/GR09/Stp4.pwm
  965. share/ugene/position_weight_matrix/UniPROBE/GR09/Sum1.pwm
  966. share/ugene/position_weight_matrix/UniPROBE/GR09/Sut2.pwm
  967. share/ugene/position_weight_matrix/UniPROBE/GR09/Tbf1.pwm
  968. share/ugene/position_weight_matrix/UniPROBE/GR09/Tbs1.pwm
  969. share/ugene/position_weight_matrix/UniPROBE/GR09/Tea1.pwm
  970. share/ugene/position_weight_matrix/UniPROBE/GR09/Tec1.pwm
  971. share/ugene/position_weight_matrix/UniPROBE/GR09/Tye7.pwm
  972. share/ugene/position_weight_matrix/UniPROBE/GR09/Ume6.pwm
  973. share/ugene/position_weight_matrix/UniPROBE/GR09/Usv1.pwm
  974. share/ugene/position_weight_matrix/UniPROBE/GR09/Xbp1.pwm
  975. share/ugene/position_weight_matrix/UniPROBE/GR09/Yap1.pwm
  976. share/ugene/position_weight_matrix/UniPROBE/GR09/Yap6.pwm
  977. share/ugene/position_weight_matrix/UniPROBE/GR09/Ybr239c.pwm
  978. share/ugene/position_weight_matrix/UniPROBE/GR09/Ydr520c.pwm
  979. share/ugene/position_weight_matrix/UniPROBE/GR09/Yer130c.pwm
  980. share/ugene/position_weight_matrix/UniPROBE/GR09/Ygr067c.pwm
  981. share/ugene/position_weight_matrix/UniPROBE/GR09/Ykl222c.pwm
  982. share/ugene/position_weight_matrix/UniPROBE/GR09/Yll054c.pwm
  983. share/ugene/position_weight_matrix/UniPROBE/GR09/Yml081w.pwm
  984. share/ugene/position_weight_matrix/UniPROBE/GR09/Ynr063w.pwm
  985. share/ugene/position_weight_matrix/UniPROBE/GR09/Yox1.pwm
  986. share/ugene/position_weight_matrix/UniPROBE/GR09/Ypr013c.pwm
  987. share/ugene/position_weight_matrix/UniPROBE/GR09/Ypr015c.pwm
  988. share/ugene/position_weight_matrix/UniPROBE/GR09/Ypr196w.pwm
  989. share/ugene/position_weight_matrix/UniPROBE/GR09/Yrm1.pwm
  990. share/ugene/position_weight_matrix/UniPROBE/GR09/Yrr1.pwm
  991. share/ugene/position_weight_matrix/UniPROBE/NBT06/Cbf1.pwm
  992. share/ugene/position_weight_matrix/UniPROBE/NBT06/Ceh-22.pwm
  993. share/ugene/position_weight_matrix/UniPROBE/NBT06/Oct-1.pwm
  994. share/ugene/position_weight_matrix/UniPROBE/NBT06/Rap1.pwm
  995. share/ugene/position_weight_matrix/UniPROBE/NBT06/Zif268.pwm
  996. share/ugene/position_weight_matrix/UniPROBE/PNAS08/Cgd2_3490.pwm
  997. share/ugene/position_weight_matrix/UniPROBE/PNAS08/PF14_0633.pwm
  998. share/ugene/position_weight_matrix/UniPROBE/PNAS08/PFF0200c.pwm
  999. share/ugene/position_weight_matrix/UniPROBE/all_uniprobe.csv
  1000. share/ugene/primer3/drosophila.w.transposons.txt
  1001. share/ugene/primer3/humrep_and_simple.txt
  1002. share/ugene/primer3/rodent_ref.txt
  1003. share/ugene/primer3/rodrep_and_simple.txt
  1004. share/ugene/query_samples/RepeatsWithORF.uql
  1005. share/ugene/query_samples/SimpleGene.uql
  1006. share/ugene/samples/ABIF/A01.abi
  1007. share/ugene/samples/ACE/BL060C3.ace
  1008. share/ugene/samples/ACE/K26.ace
  1009. share/ugene/samples/APR/DNA.apr
  1010. share/ugene/samples/APR/gyrA.apr
  1011. share/ugene/samples/Assembly/chrM.fa
  1012. share/ugene/samples/Assembly/chrM.sam
  1013. share/ugene/samples/Assembly/chrM.sorted.bam
  1014. share/ugene/samples/CLUSTALW/COI.aln
  1015. share/ugene/samples/CLUSTALW/HIV-1.aln
  1016. share/ugene/samples/CLUSTALW/ty3.aln.gz
  1017. share/ugene/samples/EMBL/AF177870.emb
  1018. share/ugene/samples/EMBL/AL000263.emb
  1019. share/ugene/samples/FASTA/human_T1.fa
  1020. share/ugene/samples/FASTQ/eas.fastq
  1021. share/ugene/samples/GFF/5prime_utr_intron_A20.gff
  1022. share/ugene/samples/GFF/5prime_utr_intron_A21.gff
  1023. share/ugene/samples/Genbank/CVU55762.gb
  1024. share/ugene/samples/Genbank/NC_014267.1.gb
  1025. share/ugene/samples/Genbank/PBR322.gb
  1026. share/ugene/samples/Genbank/murine.gb
  1027. share/ugene/samples/Genbank/sars.gb
  1028. share/ugene/samples/HMM/aligment15900.hmm
  1029. share/ugene/samples/MMDB/1CRN.prt
  1030. share/ugene/samples/MMDB/2JQS.prt
  1031. share/ugene/samples/MSF/HMA.msf
  1032. share/ugene/samples/MSF/lipid8.msf
  1033. share/ugene/samples/MSF/pla2_20.msf
  1034. share/ugene/samples/Newick/COI.nwk
  1035. share/ugene/samples/PDB/1CF7.PDB
  1036. share/ugene/samples/PDB/1CRN.PDB
  1037. share/ugene/samples/PDB/3INS.PDB
  1038. share/ugene/samples/Raw/raw.seq
  1039. share/ugene/samples/SCF/90-JRI-07.scf
  1040. share/ugene/samples/Sanger/alignment.ugenedb
  1041. share/ugene/samples/Stockholm/CBS.sto
  1042. share/ugene/samples/Stockholm/UPSK.sto
  1043. share/ugene/samples/Swiss-Prot/D0VTW9.txt
  1044. share/ugene/samples/Swiss-Prot/P01375.txt
  1045. share/ugene/samples/Swiss-Prot/P16152.txt
  1046. share/ugene/sitecon_models/eukaryotic/CEBP_a.sitecon.gz
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  1050. share/ugene/sitecon_models/eukaryotic/E2F1.sitecon.gz
  1051. share/ugene/sitecon_models/eukaryotic/E2F1DP1sel1.sitecon.gz
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  1112. share/ugene/sitecon_models/prokaryotic/ISCR1.sitecon.gz
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  1114. share/ugene/sitecon_models/prokaryotic/LEXA.sitecon.gz
  1115. share/ugene/sitecon_models/prokaryotic/Lrp.sitecon.gz
  1116. share/ugene/sitecon_models/prokaryotic/MALT.sitecon.gz
  1117. share/ugene/sitecon_models/prokaryotic/MARA.sitecon.gz
  1118. share/ugene/sitecon_models/prokaryotic/MELR.sitecon.gz
  1119. share/ugene/sitecon_models/prokaryotic/MLC.sitecon.gz
  1120. share/ugene/sitecon_models/prokaryotic/MODE.sitecon.gz
  1121. share/ugene/sitecon_models/prokaryotic/MetJ.sitecon.gz
  1122. share/ugene/sitecon_models/prokaryotic/MetR1.sitecon.gz
  1123. share/ugene/sitecon_models/prokaryotic/NAC.sitecon.gz
  1124. share/ugene/sitecon_models/prokaryotic/NAGC_new2.sitecon.gz
  1125. share/ugene/sitecon_models/prokaryotic/NANR.sitecon.gz
  1126. share/ugene/sitecon_models/prokaryotic/NARL2.sitecon.gz
  1127. share/ugene/sitecon_models/prokaryotic/NARP.sitecon.gz
  1128. share/ugene/sitecon_models/prokaryotic/NTRC.sitecon.gz
  1129. share/ugene/sitecon_models/prokaryotic/NarL.sitecon.gz
  1130. share/ugene/sitecon_models/prokaryotic/OmpR.sitecon.gz
  1131. share/ugene/sitecon_models/prokaryotic/OxyR.sitecon.gz
  1132. share/ugene/sitecon_models/prokaryotic/PHOB.sitecon.gz
  1133. share/ugene/sitecon_models/prokaryotic/PHOP.sitecon.gz
  1134. share/ugene/sitecon_models/prokaryotic/PurR.sitecon.gz
  1135. share/ugene/sitecon_models/prokaryotic/ROB.sitecon.gz
  1136. share/ugene/sitecon_models/prokaryotic/RcsB_1core.sitecon.gz
  1137. share/ugene/sitecon_models/prokaryotic/RcsB_2core.sitecon.gz
  1138. share/ugene/sitecon_models/prokaryotic/Rob2.sitecon.gz
  1139. share/ugene/sitecon_models/prokaryotic/TORR.sitecon.gz
  1140. share/ugene/sitecon_models/prokaryotic/TRPR.sitecon.gz
  1141. share/ugene/sitecon_models/prokaryotic/TyrR.sitecon.gz
  1142. share/ugene/sitecon_models/prokaryotic/fis_new1.sitecon.gz
  1143. share/ugene/sitecon_models/prokaryotic/soxS.sitecon.gz
  1144. share/ugene/snp_scripts/SNPChIPTools.py
  1145. share/ugene/snp_scripts/pdb_uniprot_chain_map.lst.2
  1146. share/ugene/snp_scripts/protstability1d.py
  1147. share/ugene/snp_scripts/protstability3d.py
  1148. share/ugene/snp_scripts/rsnp.py
  1149. share/ugene/snp_scripts/snp2pdbsite.py
  1150. share/ugene/snp_scripts/update_d_db.py
  1151. share/ugene/translations.txt
  1152. share/ugene/weight_matrix/blosum100.txt
  1153. share/ugene/weight_matrix/blosum30.txt
  1154. share/ugene/weight_matrix/blosum35.txt
  1155. share/ugene/weight_matrix/blosum40.txt
  1156. share/ugene/weight_matrix/blosum45.txt
  1157. share/ugene/weight_matrix/blosum50.txt
  1158. share/ugene/weight_matrix/blosum55.txt
  1159. share/ugene/weight_matrix/blosum60.txt
  1160. share/ugene/weight_matrix/blosum62.txt
  1161. share/ugene/weight_matrix/blosum65.txt
  1162. share/ugene/weight_matrix/blosum70.txt
  1163. share/ugene/weight_matrix/blosum75.txt
  1164. share/ugene/weight_matrix/blosum80.txt
  1165. share/ugene/weight_matrix/blosum85.txt
  1166. share/ugene/weight_matrix/blosum90.txt
  1167. share/ugene/weight_matrix/blosumn.txt
  1168. share/ugene/weight_matrix/dayhoff.txt
  1169. share/ugene/weight_matrix/dna.txt
  1170. share/ugene/weight_matrix/gonnet.txt
  1171. share/ugene/weight_matrix/identity.txt
  1172. share/ugene/weight_matrix/match.txt
  1173. share/ugene/weight_matrix/md_10.txt
  1174. share/ugene/weight_matrix/md_20.txt
  1175. share/ugene/weight_matrix/md_40.txt
  1176. share/ugene/weight_matrix/nuc.4.4.txt
  1177. share/ugene/weight_matrix/pam10.txt
  1178. share/ugene/weight_matrix/pam100.txt
  1179. share/ugene/weight_matrix/pam110.txt
  1180. share/ugene/weight_matrix/pam120.cdi.txt
  1181. share/ugene/weight_matrix/pam120.txt
  1182. share/ugene/weight_matrix/pam130.txt
  1183. share/ugene/weight_matrix/pam140.txt
  1184. share/ugene/weight_matrix/pam150.txt
  1185. share/ugene/weight_matrix/pam160.cdi.txt
  1186. share/ugene/weight_matrix/pam160.txt
  1187. share/ugene/weight_matrix/pam170.txt
  1188. share/ugene/weight_matrix/pam180.txt
  1189. share/ugene/weight_matrix/pam190.txt
  1190. share/ugene/weight_matrix/pam20.txt
  1191. share/ugene/weight_matrix/pam200.cdi.txt
  1192. share/ugene/weight_matrix/pam200.txt
  1193. share/ugene/weight_matrix/pam210.txt
  1194. share/ugene/weight_matrix/pam220.txt
  1195. share/ugene/weight_matrix/pam230.txt
  1196. share/ugene/weight_matrix/pam240.txt
  1197. share/ugene/weight_matrix/pam250.cdi.txt
  1198. share/ugene/weight_matrix/pam250.txt
  1199. share/ugene/weight_matrix/pam260.txt
  1200. share/ugene/weight_matrix/pam270.txt
  1201. share/ugene/weight_matrix/pam280.txt
  1202. share/ugene/weight_matrix/pam290.txt
  1203. share/ugene/weight_matrix/pam30.txt
  1204. share/ugene/weight_matrix/pam300.txt
  1205. share/ugene/weight_matrix/pam310.txt
  1206. share/ugene/weight_matrix/pam320.txt
  1207. share/ugene/weight_matrix/pam330.txt
  1208. share/ugene/weight_matrix/pam340.txt
  1209. share/ugene/weight_matrix/pam350.txt
  1210. share/ugene/weight_matrix/pam360.txt
  1211. share/ugene/weight_matrix/pam370.txt
  1212. share/ugene/weight_matrix/pam380.txt
  1213. share/ugene/weight_matrix/pam390.txt
  1214. share/ugene/weight_matrix/pam40.cdi.txt
  1215. share/ugene/weight_matrix/pam40.txt
  1216. share/ugene/weight_matrix/pam400.txt
  1217. share/ugene/weight_matrix/pam410.txt
  1218. share/ugene/weight_matrix/pam420.txt
  1219. share/ugene/weight_matrix/pam430.txt
  1220. share/ugene/weight_matrix/pam440.txt
  1221. share/ugene/weight_matrix/pam450.txt
  1222. share/ugene/weight_matrix/pam460.txt
  1223. share/ugene/weight_matrix/pam470.txt
  1224. share/ugene/weight_matrix/pam480.txt
  1225. share/ugene/weight_matrix/pam490.txt
  1226. share/ugene/weight_matrix/pam50.txt
  1227. share/ugene/weight_matrix/pam500.txt
  1228. share/ugene/weight_matrix/pam60.txt
  1229. share/ugene/weight_matrix/pam70.txt
  1230. share/ugene/weight_matrix/pam80.cdi.txt
  1231. share/ugene/weight_matrix/pam80.txt
  1232. share/ugene/weight_matrix/pam90.txt
  1233. share/ugene/weight_matrix/rna.txt
  1234. share/ugene/weight_matrix/vtml160.txt
  1235. share/ugene/weight_matrix/vtml200.txt
  1236. share/ugene/workflow_samples/Alignment/basic_align.uwl
  1237. share/ugene/workflow_samples/Alignment/extract_msa_consensus_as_seq.uwl
  1238. share/ugene/workflow_samples/Alignment/extract_msa_consensus_as_text.uwl
  1239. share/ugene/workflow_samples/Conversions/faqual2fastq.uwl
  1240. share/ugene/workflow_samples/Conversions/msa2clustal.uwl
  1241. share/ugene/workflow_samples/Conversions/query2alignment.uwl
  1242. share/ugene/workflow_samples/Conversions/seq2gen.uwl
  1243. share/ugene/workflow_samples/Custom elements/casava-fastq-filter.uwl
  1244. share/ugene/workflow_samples/Custom elements/fastq-trimmer.uwl
  1245. share/ugene/workflow_samples/Custom elements/script-dump-sequence-info.uwl
  1246. share/ugene/workflow_samples/Custom elements/script-linkdata-fetch-seq.uwl
  1247. share/ugene/workflow_samples/Custom elements/script-quality-filter.uwl
  1248. share/ugene/workflow_samples/Data marking/annotation_marker.uwl
  1249. share/ugene/workflow_samples/Data marking/length_marker.uwl
  1250. share/ugene/workflow_samples/Data merging/find-substrings.uwl
  1251. share/ugene/workflow_samples/Data merging/merge-sequence.uwl
  1252. share/ugene/workflow_samples/Data merging/tfbs.uwl
  1253. share/ugene/workflow_samples/HMMER/build-test-HMM.uwl
  1254. share/ugene/workflow_samples/HMMER/searchHMM.uwl
  1255. share/ugene/workflow_samples/NGS/chipseq_coverage.uwl
  1256. share/ugene/workflow_samples/NGS/cistrome.uwl
  1257. share/ugene/workflow_samples/NGS/cistrome/chip_seq.uwl
  1258. share/ugene/workflow_samples/NGS/cistrome/chip_seq_with_control.uwl
  1259. share/ugene/workflow_samples/NGS/consensus.uwl
  1260. share/ugene/workflow_samples/NGS/extract_coverage.uwl
  1261. share/ugene/workflow_samples/NGS/extract_transcript_seq.uwl
  1262. share/ugene/workflow_samples/NGS/fastqc.uwl
  1263. share/ugene/workflow_samples/NGS/from_tools_menu_only/ngs_assembly.uwl
  1264. share/ugene/workflow_samples/NGS/from_tools_menu_only/ngs_classification.uwl
  1265. share/ugene/workflow_samples/NGS/ngs_assembly_illumina_pe.uwl
  1266. share/ugene/workflow_samples/NGS/ngs_assembly_illumina_pe_nanopore.uwl
  1267. share/ugene/workflow_samples/NGS/ngs_assembly_illumina_se.uwl
  1268. share/ugene/workflow_samples/NGS/ngs_classification/ngs_classification_de_novo/ngs_classification_de_novo_paired.uwl
  1269. share/ugene/workflow_samples/NGS/ngs_classification/ngs_classification_de_novo/ngs_classification_de_novo_single.uwl
  1270. share/ugene/workflow_samples/NGS/ngs_classification/ngs_classification_parallel/ngs_classification_parallel_paired.uwl
  1271. share/ugene/workflow_samples/NGS/ngs_classification/ngs_classification_parallel/ngs_classification_parallel_single.uwl
  1272. share/ugene/workflow_samples/NGS/ngs_classification/ngs_classification_serial/ngs_classification_serial_paired.uwl
  1273. share/ugene/workflow_samples/NGS/ngs_classification/ngs_classification_serial/ngs_classification_serial_single.uwl
  1274. share/ugene/workflow_samples/NGS/ngs_classification_de_novo.uwl
  1275. share/ugene/workflow_samples/NGS/ngs_classification_parallel.uwl
  1276. share/ugene/workflow_samples/NGS/ngs_classification_serial.uwl
  1277. share/ugene/workflow_samples/NGS/ngs_transcriptomics_tophat_stringtie.uwl
  1278. share/ugene/workflow_samples/NGS/ngs_transcriptomics_tuxedo.uwl
  1279. share/ugene/workflow_samples/NGS/ngs_variant_annotation.uwl
  1280. share/ugene/workflow_samples/NGS/ngs_variant_calling.uwl
  1281. share/ugene/workflow_samples/NGS/ngs_variant_calling_full.uwl
  1282. share/ugene/workflow_samples/NGS/raw_chip.uwl
  1283. share/ugene/workflow_samples/NGS/raw_dna.uwl
  1284. share/ugene/workflow_samples/NGS/raw_ngs/chipseq/chipseq_paired.uwl
  1285. share/ugene/workflow_samples/NGS/raw_ngs/chipseq/chipseq_single.uwl
  1286. share/ugene/workflow_samples/NGS/raw_ngs/dnaseq/dna_paired.uwl
  1287. share/ugene/workflow_samples/NGS/raw_ngs/dnaseq/dna_single.uwl
  1288. share/ugene/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_filtration_paired.uwl
  1289. share/ugene/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_filtration_single.uwl
  1290. share/ugene/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_paired.uwl
  1291. share/ugene/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_single.uwl
  1292. share/ugene/workflow_samples/NGS/raw_rna.uwl
  1293. share/ugene/workflow_samples/NGS/tuxedo/tuxedo_main.uwl
  1294. share/ugene/workflow_samples/NGS/tuxedo/tuxedo_main_paired.uwl
  1295. share/ugene/workflow_samples/NGS/tuxedo/tuxedo_no_novel_transcr.uwl
  1296. share/ugene/workflow_samples/NGS/tuxedo/tuxedo_no_novel_transcr_paired.uwl
  1297. share/ugene/workflow_samples/NGS/tuxedo/tuxedo_single_dataset.uwl
  1298. share/ugene/workflow_samples/NGS/tuxedo/tuxedo_single_dataset_paired.uwl
  1299. share/ugene/workflow_samples/NGS/unmapped_reads.uwl
  1300. share/ugene/workflow_samples/Sanger sequencing/trim-and-align.uwl
  1301. share/ugene/workflow_samples/Scenarios/filter_matched.uwl
  1302. share/ugene/workflow_samples/Scenarios/find_inverted_repeats.uwl
  1303. share/ugene/workflow_samples/Scenarios/find_sequences.uwl
  1304. share/ugene/workflow_samples/Scenarios/gene_by_gene_report.uwl
  1305. share/ugene/workflow_samples/Scenarios/group_primers_pairs.uwl
  1306. share/ugene/workflow_samples/Scenarios/intersect_annotations.uwl
  1307. share/ugene/workflow_samples/Scenarios/length_filter.uwl
  1308. share/ugene/workflow_samples/Scenarios/merge_sequence_annotation.uwl
  1309. share/ugene/workflow_samples/Scenarios/pcr.uwl
  1310. share/ugene/workflow_samples/Scenarios/remote_blasting.uwl
  1311. share/ugene/workflow_samples/Scenarios/translate_seq_and_compl.uwl
  1312. share/ugene/workflow_samples/Transcriptomics/SearchTFBS.uwl
  1313. share/ugene/workflow_samples/users/CASAVA FASTQ filter.usa
  1314. share/ugene/workflow_samples/users/Dump sequence info.usa
  1315. share/ugene/workflow_samples/users/FASTQ Trimmer.usa
  1316. share/ugene/workflow_samples/users/Get the first half of sequence.usa
  1317. share/ugene/workflow_samples/users/Get the second half of sequence.usa
  1318. share/ugene/workflow_samples/users/LengthMarker.usa
  1319. share/ugene/workflow_samples/users/LinkData Fetch.usa
  1320. share/ugene/workflow_samples/users/QualityFilter.usa
  1321. share/ugene/workflow_samples/users/Read one sequence.usa
  1322. @owner
  1323. @group
  1324. @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
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: ugene
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1633934483 SHA256 (ugeneunipro-ugene-40.1_GH0.tar.gz) = 92b954449f697957c6b6b2da803ba6ae9ad546f44c584bbb2ab8600ac8b45a6e SIZE (ugeneunipro-ugene-40.1_GH0.tar.gz) = 28791083

Packages (timestamps in pop-ups are UTC):
ugene
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest-40.1_1--40.1_1---
FreeBSD:13:quarterly-40.1--40.1---
FreeBSD:14:latest-40.1_1--40.1_1---
FreeBSD:14:quarterly-40.1--40.1---
FreeBSD:15:latest-40.1_1n/a-n/a---
FreeBSD:15:quarterly--n/a-n/a---
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 : devel/qt5-buildtools
  8. lrelease : devel/qt5-linguisttools
  9. qt5-qmake>=5.15 : 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:
===> The following configuration options are available for ugene-40.1_1: OPENCL=off: Heterogeneous computing via OpenCL ===> Use 'make config' to modify these settings
Options name:
biology_ugene
USES:
desktop-file-utils gl qmake qt:5 shared-mime-info sqlite xorg
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: 60

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
40.1_1
10 Jan 2024 08:16:01
commit hash: 1b819e486953bae191a4b8f0da175b55cb6c3070commit hash: 1b819e486953bae191a4b8f0da175b55cb6c3070commit hash: 1b819e486953bae191a4b8f0da175b55cb6c3070commit hash: 1b819e486953bae191a4b8f0da175b55cb6c3070 files touched by this commit
Baptiste Daroussin (bapt) search for other commits by this committer
MAN?PREFIX: eleminate its usage  and move man to share/man
40.1
11 Sep 2022 10:20:14
commit hash: ddae4e92d8313a1461145e3b4f0232fe463feaeecommit hash: ddae4e92d8313a1461145e3b4f0232fe463feaeecommit hash: ddae4e92d8313a1461145e3b4f0232fe463feaeecommit hash: ddae4e92d8313a1461145e3b4f0232fe463feaee files touched by this commit
Felix Palmen (zirias) search for other commits by this committer
Mk/Uses: always use colon for build/run suffix

Most USES use a colon for build/run(/test) suffixes. Change kde.mk,
qt.mk and pyqt.mk to do the same, and update all ports using that.

Document in CHANGES.

PR:			266034
Exp-run by:		antoine
Approved by:		tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D36349
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
40.1
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
40.1
04 Aug 2022 16:35:24
commit hash: 5d1325cd1bad647d66d9cffb7dc0e5ee57e122e5commit hash: 5d1325cd1bad647d66d9cffb7dc0e5ee57e122e5commit hash: 5d1325cd1bad647d66d9cffb7dc0e5ee57e122e5commit hash: 5d1325cd1bad647d66d9cffb7dc0e5ee57e122e5 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/ugene: Correct BROKEN message

Approved by:	portmgr (blanket)
40.1
04 Aug 2022 07:41:24
commit hash: 34c51b63d7ff1399ba51c26cd4ab08ef73d5d335commit hash: 34c51b63d7ff1399ba51c26cd4ab08ef73d5d335commit hash: 34c51b63d7ff1399ba51c26cd4ab08ef73d5d335commit hash: 34c51b63d7ff1399ba51c26cd4ab08ef73d5d335 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/ugene: Broken on systems where OpenMP isn't enabled

Reported by:	fallout
Approved by:	portmgr (blanket)
40.1
20 Jul 2022 14:20:57
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
(Only the first 15 lines of the commit message are shown above View all of this commit message)
40.1
14 Oct 2021 11:23:37
commit hash: e409be37a880805890a6a3ba0be4aed22042f25bcommit hash: e409be37a880805890a6a3ba0be4aed22042f25bcommit hash: e409be37a880805890a6a3ba0be4aed22042f25bcommit hash: e409be37a880805890a6a3ba0be4aed22042f25b files touched by this commit
Alexey Dokuchaev (danfe) search for other commits by this committer
biology/ugene: update UniPro UGENE to version 40.1 (bugfix release).
40.0
16 Sep 2021 09:48:26
commit hash: 299862ff2afc17f5a415843ba9fc87ee6074fa87commit hash: 299862ff2afc17f5a415843ba9fc87ee6074fa87commit hash: 299862ff2afc17f5a415843ba9fc87ee6074fa87commit hash: 299862ff2afc17f5a415843ba9fc87ee6074fa87 files touched by this commit
Alexey Dokuchaev (danfe) search for other commits by this committer
biology/ugene: update Unipro UGENE to version 40.0.
39.0
25 Jun 2021 17:56:47
commit hash: 05f96c80f8f5cde88a25a3f71a1b6248dd84827acommit hash: 05f96c80f8f5cde88a25a3f71a1b6248dd84827acommit hash: 05f96c80f8f5cde88a25a3f71a1b6248dd84827acommit hash: 05f96c80f8f5cde88a25a3f71a1b6248dd84827a files touched by this commit
Alexey Dokuchaev (danfe) search for other commits by this committer
biology/ugene: update Unipro UGENE to version 39.0.
38.1_1
22 Jun 2021 18:53:08
commit hash: da3162c7c9f01912ba1940e188b253f2b5c7ba77commit hash: da3162c7c9f01912ba1940e188b253f2b5c7ba77commit hash: da3162c7c9f01912ba1940e188b253f2b5c7ba77commit hash: da3162c7c9f01912ba1940e188b253f2b5c7ba77 files touched by this commit
Kevin Bowling (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
38.1
18 May 2021 15:24:55
commit hash: 6464fe05fe9d896e130503dfc4533d946d787e0fcommit hash: 6464fe05fe9d896e130503dfc4533d946d787e0fcommit hash: 6464fe05fe9d896e130503dfc4533d946d787e0fcommit hash: 6464fe05fe9d896e130503dfc4533d946d787e0f files touched by this commit
Alexey Dokuchaev (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
38.0
12 May 2021 11:55:32
commit hash: 4b5a5c6d9c8767e327824d8d20c8d4bf86534904commit hash: 4b5a5c6d9c8767e327824d8d20c8d4bf86534904commit hash: 4b5a5c6d9c8767e327824d8d20c8d4bf86534904commit hash: 4b5a5c6d9c8767e327824d8d20c8d4bf86534904 files touched by this commit
Dmitry Marakasov (amdmi3) search for other commits by this committer
biology/ugene: mark BROKEN (does not fetch)

Approved by:	portmgr blanket
38.0
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
38.0
23 Mar 2021 14:20:49
Revision:569026Original commit files touched by this commit
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!
37.0
19 Jan 2021 02:29:16
Revision:562006Original commit files touched by this commit
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
37.0
31 Dec 2020 13:43:10
Revision:559737Original commit files touched by this commit
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
34.0
19 May 2020 18:00:02
Revision:535875Original commit files touched by this commit
tcberner search for other commits by this committer
biology/ugene: prepare for Qt5-5.15
34.0
10 May 2020 15:42:33
Revision:534852Original commit files touched by this commit
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
1.31.0_1
05 May 2020 15:38:12
Revision:534093Original commit files touched by this commit
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)
1.31.0_1
04 Apr 2020 20:51:41
Revision:530719Original commit files touched by this commit Sanity Test Failure
antoine search for other commits by this committer
Deprecate ports broken for more than 6 months
1.31.0_1
06 Nov 2019 12:48:32
Revision:516880Original commit files touched by this commit Sanity Test Failure
antoine search for other commits by this committer
Mark a few ports BROKEN, unfetchable
1.31.0_1
04 Nov 2019 21:08:20
Revision:516742Original commit files touched by this commit
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'.
1.31.0_1
16 Jan 2019 11:13:45
Revision:490472Original commit files touched by this commit
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
(Only the first 15 lines of the commit message are shown above View all of this commit message)
1.31.0
16 Dec 2018 14:49:16
Revision:487594Original commit files touched by this commit
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
1.31.0
02 Sep 2018 20:47:15
Revision:478818Original commit files touched by this commit
jhale search for other commits by this committer
Update to 1.31.0

PR:		229463
Approved by:	Hannes Hauswedell <h2+fbsdports@fsfe.org> (maintainer)
1.22.0_3
28 Jun 2018 17:39:55
Revision:473503Original commit files touched by this commit
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
1.22.0_3
15 May 2018 18:51:51
Revision:470045Original commit files touched by this commit
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
1.22.0_2
06 Jan 2018 21:30:33
Revision:458293Original commit files touched by this commit
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.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
1.22.0_2
22 Sep 2017 10:48:29
Revision:450351Original commit files touched by this commit
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
1.22.0_2
23 May 2017 05:03:16
Revision:441503Original commit files touched by this commit
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
1.22.0_1
09 Jan 2017 13:16:50
Revision:430947Original commit files touched by this commit
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
1.22.0_1
08 Nov 2016 19:29:57
Revision:425758Original commit files touched by this commit
linimon search for other commits by this committer
The 64-bit arm arch is actually spelled 'aarch64', not 'arm64'.
1.22.0_1
08 Nov 2016 07:20:38
Revision:425689Original commit files touched by this commit
linimon search for other commits by this committer
Mark as broken on arm64.

Approved by:	portmgr (tier-2 blanket)
1.22.0_1
07 May 2016 19:38:53
Revision:414784Original commit files touched by this commit
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
1.22.0
14 Apr 2016 04:07:44
Revision:413242Original commit files touched by this commit
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.
1.17.0_1
01 Apr 2016 13:29:17
Revision:412344Original commit files touched by this commit
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
1.17.0_1
18 Aug 2015 20:02:46
Revision:394652Original commit files touched by this commit
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
1.17.0
15 Jul 2015 07:18:09
Revision:392119Original commit files touched by this commit
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)
1.16.2
28 May 2015 08:12:00
Revision:387709Original commit files touched by this commit
danfe search for other commits by this committer
Update Unipro UGENE to version 1.16.2.
1.16.1
23 Mar 2015 01:44:44
Revision:381974Original commit files touched by this commit
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
1.16.0
24 Feb 2015 11:42:54
Revision:379787Original commit files touched by this commit
danfe search for other commits by this committer
Update Unipro UGENE to version 1.16.0 (documentation was also rerolled).
1.15.1
06 Jan 2015 05:28:59
Revision:376383Original commit files touched by this commit
danfe search for other commits by this committer
Update to version 1.15.1.
1.15.0
03 Dec 2014 01:40:55
Revision:373799Original commit files touched by this commit
danfe search for other commits by this committer
Update to version 1.15.0.
1.14.2
20 Oct 2014 07:10:48
Revision:371237Original commit files touched by this commit
bapt search for other commits by this committer
Cleanup plist
1.14.2
13 Oct 2014 11:01:52
Revision:370764Original commit files touched by this commit
danfe search for other commits by this committer
Update to version 1.14.2.
1.14.0_1
10 Sep 2014 20:50:37
Revision:367888Original commit files touched by this commit
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)
1.14.0
01 Sep 2014 07:39:00
Revision:366842Original commit files touched by this commit
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)
1.13.1
04 Aug 2014 23:06:21
Revision:364067Original commit files touched by this commit
bapt search for other commits by this committer
USES=execinfo
1.13.1
07 Mar 2014 07:39:21
Revision:347340Original commit files touched by this commit
danfe search for other commits by this committer
Update to version 1.13.1.
1.13.0
30 Jan 2014 13:38:26
Revision:341837Original commit files touched by this commit
danfe search for other commits by this committer
Unbreak the fetch: one of the documentation PDF files was rerolled.
1.13.0
30 Jan 2014 13:11:41
Revision:341835Original commit files touched by this commit
decke search for other commits by this committer
- Mark BROKEN because it does not fetch
1.13.0
16 Jan 2014 17:17:16
Revision:339938Original commit files touched by this commit
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)
1.12.3
01 Nov 2013 15:20:29
Revision:332391Original commit files touched by this commit
danfe search for other commits by this committer
- Install official UGENE documentation (PDF)
- Utilize DIST_SUBDIR as now it's more than one distfile
1.12.3
31 Oct 2013 15:30:04
Revision:332256Original commit files touched by this commit
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)
1.11.4
22 Oct 2013 13:57:35
Revision:331271Original commit files touched by this commit
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)
1.11.4
20 Sep 2013 15:55:44
Revision:327709Original commit files touched by this commit
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
1.11.4
14 Aug 2013 22:35:54
Revision:324744Original commit files touched by this commit Sanity Test Failure
ak search for other commits by this committer
- Remove MAKE_JOBS_SAFE variable

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

Reported by:	QAT
1.11.4
23 Feb 2013 04:50:48
Revision:312798Original commit files touched by this commit
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: 60