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Port details on branch 2022Q2
seqtools Tools for visualising sequence alignments
4.44.1_4 biology Deleted 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 4.44.1_4Version of this port present on the latest quarterly branch.
Broken BROKEN: unfetchable
Deprecated DEPRECATED: Broken for more than 6 months
Expired This port expired on: 2020-05-05
Ignore IGNORE: is marked as broken: unfetchable
Maintainer: pi@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2013-11-10 11:01:14
Last Update: 2020-05-05 15:38:12
SVN Revision: 534093
License: GPLv3
WWW:
http://www.sanger.ac.uk/science/tools/seqtools
Description:
A suite of tools for visualising sequence alignments. Blixem is an interactive browser of pairwise alignments that have been stacked up in a "master-slave" multiple alignment; it is not a 'true' multiple alignment but a 'one-to-many' alignment. Belvu is a multiple sequence alignment viewer and phylogenetic tool. It has an extensive set of user-configurable modes to color residues by conservation or by residue type, and some basic alignment editing capabilities. Dotter is a graphical dot-matrix program for detailed comparison of two sequences. Every residue in one sequence is compared to every residue in the other, with one sequence plotted on the x-axis and the other on the y-axis. WWW: http://www.sanger.ac.uk/science/tools/seqtools
Homepage    cgit ¦ GitHub ¦ 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 (229 items)
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  1. /usr/local/share/licenses/seqtools-4.44.1_4/catalog.mk
  2. /usr/local/share/licenses/seqtools-4.44.1_4/LICENSE
  3. /usr/local/share/licenses/seqtools-4.44.1_4/GPLv3
  4. share/doc/seqtools/Belvu_manual.pdf
  5. share/doc/seqtools/Blixem_manual.pdf
  6. share/doc/seqtools/Dotter_manual.pdf
  7. share/doc/seqtools/belvu_quick_start.html
  8. share/doc/seqtools/belvu_usage.txt
  9. share/doc/seqtools/blixem_quick_start.html
  10. share/doc/seqtools/blixem_usage.txt
  11. share/doc/seqtools/dotter_quick_start.html
  12. share/doc/seqtools/dotter_usage.txt
  13. share/doc/seqtools/release_notes.html
  14. share/doc/seqtools/todo.html
  15. bin/belvu
  16. bin/blixem
  17. bin/blixemh
  18. bin/dotter
  19. include/blatSrc/ace.h
  20. include/blatSrc/aliType.h
  21. include/blatSrc/annoAssembly.h
  22. include/blatSrc/annoFilter.h
  23. include/blatSrc/annoFormatTab.h
  24. include/blatSrc/annoFormatter.h
  25. include/blatSrc/annoGrateWig.h
  26. include/blatSrc/annoGrator.h
  27. include/blatSrc/annoGratorQuery.h
  28. include/blatSrc/annoOption.h
  29. include/blatSrc/annoRow.h
  30. include/blatSrc/annoStreamBigBed.h
  31. include/blatSrc/annoStreamBigWig.h
  32. include/blatSrc/annoStreamTab.h
  33. include/blatSrc/annoStreamVcf.h
  34. include/blatSrc/annoStreamer.h
  35. include/blatSrc/apacheLog.h
  36. include/blatSrc/asParse.h
  37. include/blatSrc/axt.h
  38. include/blatSrc/bPlusTree.h
  39. include/blatSrc/bamFile.h
  40. include/blatSrc/bandExt.h
  41. include/blatSrc/base64.h
  42. include/blatSrc/basicBed.h
  43. include/blatSrc/bbiFile.h
  44. include/blatSrc/bigBed.h
  45. include/blatSrc/bigWig.h
  46. include/blatSrc/binRange.h
  47. include/blatSrc/bits.h
  48. include/blatSrc/blastParse.h
  49. include/blatSrc/boxClump.h
  50. include/blatSrc/boxLump.h
  51. include/blatSrc/bwgInternal.h
  52. include/blatSrc/cda.h
  53. include/blatSrc/cgi_build_rules.mk
  54. include/blatSrc/chain.h
  55. include/blatSrc/chainBlock.h
  56. include/blatSrc/chainConnect.h
  57. include/blatSrc/chainToAxt.h
  58. include/blatSrc/chainToPsl.h
  59. include/blatSrc/cheapcgi.h
  60. include/blatSrc/cirTree.h
  61. include/blatSrc/codebias.h
  62. include/blatSrc/common.h
  63. include/blatSrc/common.mk
  64. include/blatSrc/correlate.h
  65. include/blatSrc/crTree.h
  66. include/blatSrc/crudeali.h
  67. include/blatSrc/diGraph.h
  68. include/blatSrc/diGraph.h.97
  69. include/blatSrc/dlist.h
  70. include/blatSrc/dnaLoad.h
  71. include/blatSrc/dnaMarkov.h
  72. include/blatSrc/dnaMotif.h
  73. include/blatSrc/dnaseq.h
  74. include/blatSrc/dnautil.h
  75. include/blatSrc/dtdParse.h
  76. include/blatSrc/dyOut.h
  77. include/blatSrc/dystring.h
  78. include/blatSrc/elmTree.h
  79. include/blatSrc/emblParse.h
  80. include/blatSrc/ens.h
  81. include/blatSrc/errAbort.h
  82. include/blatSrc/errCatch.h
  83. include/blatSrc/fa.h
  84. include/blatSrc/fieldedTable.h
  85. include/blatSrc/filePath.h
  86. include/blatSrc/flydna.h
  87. include/blatSrc/fof.h
  88. include/blatSrc/fq.h
  89. include/blatSrc/fuzzyFind.h
  90. include/blatSrc/gapCalc.h
  91. include/blatSrc/gdf.h
  92. include/blatSrc/genoFind.h
  93. include/blatSrc/genomeRangeTree.h
  94. include/blatSrc/gfClientLib.h
  95. include/blatSrc/gfPcrLib.h
  96. include/blatSrc/gfWebLib.h
  97. include/blatSrc/gff.h
  98. include/blatSrc/gff3.h
  99. include/blatSrc/gfxPoly.h
  100. include/blatSrc/gifLabel.h
  101. include/blatSrc/hacTree.h
  102. include/blatSrc/hash.h
  103. include/blatSrc/hex.h
  104. include/blatSrc/hgGene.h
  105. include/blatSrc/hgap.h
  106. include/blatSrc/hgdb.h
  107. include/blatSrc/histogram.h
  108. include/blatSrc/hmac.h
  109. include/blatSrc/hmmPfamParse.h
  110. include/blatSrc/hmmstats.h
  111. include/blatSrc/htmlPage.h
  112. include/blatSrc/htmshell.h
  113. include/blatSrc/https.h
  114. include/blatSrc/intValTree.h
  115. include/blatSrc/internet.h
  116. include/blatSrc/itsa.h
  117. include/blatSrc/iupac.h
  118. include/blatSrc/jointalign.h
  119. include/blatSrc/jpegSize.h
  120. include/blatSrc/jsonParse.h
  121. include/blatSrc/jsonWrite.h
  122. include/blatSrc/keys.h
  123. include/blatSrc/knetUdc.h
  124. include/blatSrc/kxTok.h
  125. include/blatSrc/linefile.h
  126. include/blatSrc/localEnvironment.mk
  127. include/blatSrc/localmem.h
  128. include/blatSrc/log.h
  129. include/blatSrc/longToList.h
  130. include/blatSrc/maDbRep.h
  131. include/blatSrc/maToFf.h
  132. include/blatSrc/maf.h
  133. include/blatSrc/mailViaPipe.h
  134. include/blatSrc/md5.h
  135. include/blatSrc/memalloc.h
  136. include/blatSrc/memgfx.h
  137. include/blatSrc/meta.h
  138. include/blatSrc/metaWig.h
  139. include/blatSrc/mime.h
  140. include/blatSrc/net.h
  141. include/blatSrc/nib.h
  142. include/blatSrc/nibTwo.h
  143. include/blatSrc/nt4.h
  144. include/blatSrc/obscure.h
  145. include/blatSrc/oldGff.h
  146. include/blatSrc/oligoTm.h
  147. include/blatSrc/ooc.h
  148. include/blatSrc/options.h
  149. include/blatSrc/pairDistance.h
  150. include/blatSrc/pairHmm.h
  151. include/blatSrc/paraFetch.h
  152. include/blatSrc/patSpace.h
  153. include/blatSrc/peakCluster.h
  154. include/blatSrc/phyloTree.h
  155. include/blatSrc/pipeline.h
  156. include/blatSrc/portable.h
  157. include/blatSrc/psGfx.h
  158. include/blatSrc/psPoly.h
  159. include/blatSrc/pscmGfx.h
  160. include/blatSrc/psl.h
  161. include/blatSrc/pslTbl.h
  162. include/blatSrc/pslTransMap.h
  163. include/blatSrc/pthreadDoList.h
  164. include/blatSrc/pthreadWrap.h
  165. include/blatSrc/qa.h
  166. include/blatSrc/quickHeap.h
  167. include/blatSrc/quotedP.h
  168. include/blatSrc/ra.h
  169. include/blatSrc/raToStruct.h
  170. include/blatSrc/rainbow.h
  171. include/blatSrc/rangeTree.h
  172. include/blatSrc/rbTree.h
  173. include/blatSrc/regexHelper.h
  174. include/blatSrc/repMask.h
  175. include/blatSrc/rle.h
  176. include/blatSrc/rnautil.h
  177. include/blatSrc/rql.h
  178. include/blatSrc/rudp.h
  179. include/blatSrc/scoreWindow.h
  180. include/blatSrc/seg.h
  181. include/blatSrc/seqOut.h
  182. include/blatSrc/seqStats.h
  183. include/blatSrc/shaRes.h
  184. include/blatSrc/sig.h
  185. include/blatSrc/slog.h
  186. include/blatSrc/snof.h
  187. include/blatSrc/snofmake.h
  188. include/blatSrc/spaceSaver.h
  189. include/blatSrc/spacedColumn.h
  190. include/blatSrc/spacedSeed.h
  191. include/blatSrc/splatAli.h
  192. include/blatSrc/splix.h
  193. include/blatSrc/sqlList.h
  194. include/blatSrc/sqlNum.h
  195. include/blatSrc/subText.h
  196. include/blatSrc/sufa.h
  197. include/blatSrc/sufx.h
  198. include/blatSrc/supStitch.h
  199. include/blatSrc/synQueue.h
  200. include/blatSrc/tabRow.h
  201. include/blatSrc/textOut.h
  202. include/blatSrc/tokenizer.h
  203. include/blatSrc/trans3.h
  204. include/blatSrc/trix.h
  205. include/blatSrc/twoBit.h
  206. include/blatSrc/udc.h
  207. include/blatSrc/unfin.h
  208. include/blatSrc/userApp.mk
  209. include/blatSrc/vGfx.h
  210. include/blatSrc/vcf.h
  211. include/blatSrc/vcfBits.h
  212. include/blatSrc/verbose.h
  213. include/blatSrc/wormdna.h
  214. include/blatSrc/xAli.h
  215. include/blatSrc/xa.h
  216. include/blatSrc/xap.h
  217. include/blatSrc/xenalign.h
  218. include/blatSrc/xmlEscape.h
  219. include/blatSrc/xp.h
  220. include/blatSrc/zlibFace.h
  221. include/gbtools/gbtools.hpp
  222. include/gbtools/gbtoolsCurl.hpp
  223. include/gbtools/gbtoolsGUI.hpp
  224. include/gbtools/gbtoolsPfetch.hpp
  225. include/gbtools/gbtoolsTrackhub.hpp
  226. include/gbtools/gbtoolsUtils.hpp
  227. include/json/json-forwards.h
  228. include/json/json.h
  229. lib/libgbtools.a
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Dependency lines:
  • seqtools>0:biology/seqtools
No installation instructions:
This port has been deleted.
PKGNAME: seqtools
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1478810582 SHA256 (seqtools-4.44.1.tar.gz) = 0e1dd7087d1180e434f0ea1aac21b8dfb5261195581ec3ba012abf0d1e39daa9 SIZE (seqtools-4.44.1.tar.gz) = 6922888

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Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. msgfmt : devel/gettext-tools
  2. pkgconf>=1.3.0_1 : devel/pkgconf
  3. as : devel/binutils
  4. x11.pc : x11/libX11
Runtime dependencies:
  1. x11.pc : x11/libX11
Library dependencies:
  1. libcurl.so : ftp/curl
  2. libsqlite3.so : databases/sqlite3
  3. libfontconfig.so : x11-fonts/fontconfig
  4. libfreetype.so : print/freetype2
  5. libintl.so : devel/gettext-runtime
  6. libatk-1.0.so : accessibility/atk
  7. libcairo.so : graphics/cairo
  8. libgdk_pixbuf-2.0.so : graphics/gdk-pixbuf2
  9. libglib-2.0.so : devel/glib20
  10. libintl.so : devel/gettext-runtime
  11. libgtk-x11-2.0.so : x11-toolkits/gtk20
  12. libpango-1.0.so : x11-toolkits/pango
There are no ports dependent upon this port

Configuration Options:
===> The following configuration options are available for seqtools-4.44.1_4: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings
Options name:
N/A
USES:
compiler:c++14-lang gettext gnome libtool pkgconfig xorg
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
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  1. ftp://ftp.sanger.ac.uk/pub4/resources/software/seqtools/PRODUCTION/
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There are no commits on branch 2022Q2 for this port