miga-base 1.2.15.2 → 1.2.15.3

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Files changed (304) hide show
  1. checksums.yaml +4 -4
  2. data/lib/miga/cli/action/download/gtdb.rb +4 -1
  3. data/lib/miga/cli/action/gtdb_get.rb +4 -0
  4. data/lib/miga/remote_dataset/download.rb +3 -2
  5. data/lib/miga/remote_dataset.rb +25 -7
  6. data/lib/miga/taxonomy.rb +6 -0
  7. data/lib/miga/version.rb +2 -2
  8. metadata +6 -302
  9. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Archaea_SCG.hmm +0 -41964
  10. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Bacteria_SCG.hmm +0 -32439
  11. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Complete_SCG_DB.hmm +0 -62056
  12. data/utils/FastAAI/FastAAI +0 -3659
  13. data/utils/FastAAI/FastAAI-legacy/FastAAI +0 -1336
  14. data/utils/FastAAI/FastAAI-legacy/kAAI_v1.0_virus.py +0 -1296
  15. data/utils/FastAAI/README.md +0 -84
  16. data/utils/enveomics/Docs/recplot2.md +0 -244
  17. data/utils/enveomics/Examples/aai-matrix.bash +0 -66
  18. data/utils/enveomics/Examples/ani-matrix.bash +0 -66
  19. data/utils/enveomics/Examples/essential-phylogeny.bash +0 -105
  20. data/utils/enveomics/Examples/unus-genome-phylogeny.bash +0 -100
  21. data/utils/enveomics/LICENSE.txt +0 -73
  22. data/utils/enveomics/Makefile +0 -52
  23. data/utils/enveomics/Manifest/Tasks/aasubs.json +0 -103
  24. data/utils/enveomics/Manifest/Tasks/blasttab.json +0 -790
  25. data/utils/enveomics/Manifest/Tasks/distances.json +0 -161
  26. data/utils/enveomics/Manifest/Tasks/fasta.json +0 -802
  27. data/utils/enveomics/Manifest/Tasks/fastq.json +0 -291
  28. data/utils/enveomics/Manifest/Tasks/graphics.json +0 -126
  29. data/utils/enveomics/Manifest/Tasks/mapping.json +0 -137
  30. data/utils/enveomics/Manifest/Tasks/ogs.json +0 -382
  31. data/utils/enveomics/Manifest/Tasks/other.json +0 -906
  32. data/utils/enveomics/Manifest/Tasks/remote.json +0 -355
  33. data/utils/enveomics/Manifest/Tasks/sequence-identity.json +0 -650
  34. data/utils/enveomics/Manifest/Tasks/tables.json +0 -308
  35. data/utils/enveomics/Manifest/Tasks/trees.json +0 -68
  36. data/utils/enveomics/Manifest/Tasks/variants.json +0 -111
  37. data/utils/enveomics/Manifest/categories.json +0 -165
  38. data/utils/enveomics/Manifest/examples.json +0 -162
  39. data/utils/enveomics/Manifest/tasks.json +0 -4
  40. data/utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash +0 -69
  41. data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +0 -1
  42. data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +0 -1
  43. data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +0 -1
  44. data/utils/enveomics/Pipelines/assembly.pbs/README.md +0 -189
  45. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash +0 -112
  46. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash +0 -23
  47. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash +0 -44
  48. data/utils/enveomics/Pipelines/assembly.pbs/RUNME.bash +0 -50
  49. data/utils/enveomics/Pipelines/assembly.pbs/kSelector.R +0 -37
  50. data/utils/enveomics/Pipelines/assembly.pbs/newbler.pbs +0 -68
  51. data/utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl +0 -49
  52. data/utils/enveomics/Pipelines/assembly.pbs/soap.pbs +0 -80
  53. data/utils/enveomics/Pipelines/assembly.pbs/stats.pbs +0 -57
  54. data/utils/enveomics/Pipelines/assembly.pbs/velvet.pbs +0 -63
  55. data/utils/enveomics/Pipelines/blast.pbs/01.pbs.bash +0 -38
  56. data/utils/enveomics/Pipelines/blast.pbs/02.pbs.bash +0 -73
  57. data/utils/enveomics/Pipelines/blast.pbs/03.pbs.bash +0 -21
  58. data/utils/enveomics/Pipelines/blast.pbs/BlastTab.recover_job.pl +0 -72
  59. data/utils/enveomics/Pipelines/blast.pbs/CONFIG.mock.bash +0 -98
  60. data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +0 -1
  61. data/utils/enveomics/Pipelines/blast.pbs/README.md +0 -127
  62. data/utils/enveomics/Pipelines/blast.pbs/RUNME.bash +0 -109
  63. data/utils/enveomics/Pipelines/blast.pbs/TASK.check.bash +0 -128
  64. data/utils/enveomics/Pipelines/blast.pbs/TASK.dry.bash +0 -16
  65. data/utils/enveomics/Pipelines/blast.pbs/TASK.eo.bash +0 -22
  66. data/utils/enveomics/Pipelines/blast.pbs/TASK.pause.bash +0 -26
  67. data/utils/enveomics/Pipelines/blast.pbs/TASK.run.bash +0 -89
  68. data/utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash +0 -29
  69. data/utils/enveomics/Pipelines/idba.pbs/README.md +0 -49
  70. data/utils/enveomics/Pipelines/idba.pbs/RUNME.bash +0 -95
  71. data/utils/enveomics/Pipelines/idba.pbs/run.pbs +0 -56
  72. data/utils/enveomics/Pipelines/trim.pbs/README.md +0 -54
  73. data/utils/enveomics/Pipelines/trim.pbs/RUNME.bash +0 -70
  74. data/utils/enveomics/Pipelines/trim.pbs/run.pbs +0 -130
  75. data/utils/enveomics/README.md +0 -42
  76. data/utils/enveomics/Scripts/AAsubs.log2ratio.rb +0 -171
  77. data/utils/enveomics/Scripts/Aln.cat.rb +0 -221
  78. data/utils/enveomics/Scripts/Aln.convert.pl +0 -35
  79. data/utils/enveomics/Scripts/AlphaDiversity.pl +0 -152
  80. data/utils/enveomics/Scripts/BedGraph.tad.rb +0 -93
  81. data/utils/enveomics/Scripts/BedGraph.window.rb +0 -71
  82. data/utils/enveomics/Scripts/BlastPairwise.AAsubs.pl +0 -102
  83. data/utils/enveomics/Scripts/BlastTab.addlen.rb +0 -63
  84. data/utils/enveomics/Scripts/BlastTab.advance.bash +0 -48
  85. data/utils/enveomics/Scripts/BlastTab.best_hit_sorted.pl +0 -55
  86. data/utils/enveomics/Scripts/BlastTab.catsbj.pl +0 -104
  87. data/utils/enveomics/Scripts/BlastTab.cogCat.rb +0 -76
  88. data/utils/enveomics/Scripts/BlastTab.filter.pl +0 -47
  89. data/utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl +0 -194
  90. data/utils/enveomics/Scripts/BlastTab.metaxaPrep.pl +0 -104
  91. data/utils/enveomics/Scripts/BlastTab.pairedHits.rb +0 -157
  92. data/utils/enveomics/Scripts/BlastTab.recplot2.R +0 -48
  93. data/utils/enveomics/Scripts/BlastTab.seqdepth.pl +0 -86
  94. data/utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl +0 -119
  95. data/utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl +0 -86
  96. data/utils/enveomics/Scripts/BlastTab.subsample.pl +0 -47
  97. data/utils/enveomics/Scripts/BlastTab.sumPerHit.pl +0 -114
  98. data/utils/enveomics/Scripts/BlastTab.taxid2taxrank.pl +0 -90
  99. data/utils/enveomics/Scripts/BlastTab.topHits_sorted.rb +0 -123
  100. data/utils/enveomics/Scripts/Chao1.pl +0 -97
  101. data/utils/enveomics/Scripts/CharTable.classify.rb +0 -234
  102. data/utils/enveomics/Scripts/EBIseq2tax.rb +0 -83
  103. data/utils/enveomics/Scripts/FastA.N50.pl +0 -60
  104. data/utils/enveomics/Scripts/FastA.extract.rb +0 -152
  105. data/utils/enveomics/Scripts/FastA.filter.pl +0 -52
  106. data/utils/enveomics/Scripts/FastA.filterLen.pl +0 -28
  107. data/utils/enveomics/Scripts/FastA.filterN.pl +0 -60
  108. data/utils/enveomics/Scripts/FastA.fragment.rb +0 -100
  109. data/utils/enveomics/Scripts/FastA.gc.pl +0 -42
  110. data/utils/enveomics/Scripts/FastA.interpose.pl +0 -93
  111. data/utils/enveomics/Scripts/FastA.length.pl +0 -38
  112. data/utils/enveomics/Scripts/FastA.mask.rb +0 -89
  113. data/utils/enveomics/Scripts/FastA.per_file.pl +0 -36
  114. data/utils/enveomics/Scripts/FastA.qlen.pl +0 -57
  115. data/utils/enveomics/Scripts/FastA.rename.pl +0 -65
  116. data/utils/enveomics/Scripts/FastA.revcom.pl +0 -23
  117. data/utils/enveomics/Scripts/FastA.sample.rb +0 -98
  118. data/utils/enveomics/Scripts/FastA.slider.pl +0 -85
  119. data/utils/enveomics/Scripts/FastA.split.pl +0 -55
  120. data/utils/enveomics/Scripts/FastA.split.rb +0 -79
  121. data/utils/enveomics/Scripts/FastA.subsample.pl +0 -131
  122. data/utils/enveomics/Scripts/FastA.tag.rb +0 -65
  123. data/utils/enveomics/Scripts/FastA.toFastQ.rb +0 -69
  124. data/utils/enveomics/Scripts/FastA.wrap.rb +0 -48
  125. data/utils/enveomics/Scripts/FastQ.filter.pl +0 -54
  126. data/utils/enveomics/Scripts/FastQ.interpose.pl +0 -90
  127. data/utils/enveomics/Scripts/FastQ.maskQual.rb +0 -89
  128. data/utils/enveomics/Scripts/FastQ.offset.pl +0 -90
  129. data/utils/enveomics/Scripts/FastQ.split.pl +0 -53
  130. data/utils/enveomics/Scripts/FastQ.tag.rb +0 -70
  131. data/utils/enveomics/Scripts/FastQ.test-error.rb +0 -81
  132. data/utils/enveomics/Scripts/FastQ.toFastA.awk +0 -24
  133. data/utils/enveomics/Scripts/GFF.catsbj.pl +0 -127
  134. data/utils/enveomics/Scripts/GenBank.add_fields.rb +0 -84
  135. data/utils/enveomics/Scripts/HMM.essential.rb +0 -351
  136. data/utils/enveomics/Scripts/HMM.haai.rb +0 -168
  137. data/utils/enveomics/Scripts/HMMsearch.extractIds.rb +0 -83
  138. data/utils/enveomics/Scripts/JPlace.distances.rb +0 -88
  139. data/utils/enveomics/Scripts/JPlace.to_iToL.rb +0 -320
  140. data/utils/enveomics/Scripts/M5nr.getSequences.rb +0 -81
  141. data/utils/enveomics/Scripts/MeTaxa.distribution.pl +0 -198
  142. data/utils/enveomics/Scripts/MyTaxa.fragsByTax.pl +0 -35
  143. data/utils/enveomics/Scripts/MyTaxa.seq-taxrank.rb +0 -49
  144. data/utils/enveomics/Scripts/NCBIacc2tax.rb +0 -92
  145. data/utils/enveomics/Scripts/Newick.autoprune.R +0 -27
  146. data/utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl +0 -228
  147. data/utils/enveomics/Scripts/RecPlot2.compareIdentities.R +0 -32
  148. data/utils/enveomics/Scripts/RefSeq.download.bash +0 -48
  149. data/utils/enveomics/Scripts/SRA.download.bash +0 -55
  150. data/utils/enveomics/Scripts/TRIBS.plot-test.R +0 -36
  151. data/utils/enveomics/Scripts/TRIBS.test.R +0 -39
  152. data/utils/enveomics/Scripts/Table.barplot.R +0 -31
  153. data/utils/enveomics/Scripts/Table.df2dist.R +0 -30
  154. data/utils/enveomics/Scripts/Table.filter.pl +0 -61
  155. data/utils/enveomics/Scripts/Table.merge.pl +0 -77
  156. data/utils/enveomics/Scripts/Table.prefScore.R +0 -60
  157. data/utils/enveomics/Scripts/Table.replace.rb +0 -69
  158. data/utils/enveomics/Scripts/Table.round.rb +0 -63
  159. data/utils/enveomics/Scripts/Table.split.pl +0 -57
  160. data/utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb +0 -227
  161. data/utils/enveomics/Scripts/VCF.KaKs.rb +0 -147
  162. data/utils/enveomics/Scripts/VCF.SNPs.rb +0 -88
  163. data/utils/enveomics/Scripts/aai.rb +0 -421
  164. data/utils/enveomics/Scripts/ani.rb +0 -362
  165. data/utils/enveomics/Scripts/anir.rb +0 -137
  166. data/utils/enveomics/Scripts/clust.rand.rb +0 -102
  167. data/utils/enveomics/Scripts/gi2tax.rb +0 -103
  168. data/utils/enveomics/Scripts/in_silico_GA_GI.pl +0 -96
  169. data/utils/enveomics/Scripts/lib/data/dupont_2012_essential.hmm.gz +0 -0
  170. data/utils/enveomics/Scripts/lib/data/lee_2019_essential.hmm.gz +0 -0
  171. data/utils/enveomics/Scripts/lib/enveomics.R +0 -1
  172. data/utils/enveomics/Scripts/lib/enveomics_rb/anir.rb +0 -293
  173. data/utils/enveomics/Scripts/lib/enveomics_rb/bm_set.rb +0 -175
  174. data/utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb +0 -24
  175. data/utils/enveomics/Scripts/lib/enveomics_rb/errors.rb +0 -17
  176. data/utils/enveomics/Scripts/lib/enveomics_rb/gmm_em.rb +0 -30
  177. data/utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb +0 -253
  178. data/utils/enveomics/Scripts/lib/enveomics_rb/match.rb +0 -88
  179. data/utils/enveomics/Scripts/lib/enveomics_rb/og.rb +0 -182
  180. data/utils/enveomics/Scripts/lib/enveomics_rb/rbm.rb +0 -49
  181. data/utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb +0 -74
  182. data/utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb +0 -237
  183. data/utils/enveomics/Scripts/lib/enveomics_rb/stats/rand.rb +0 -31
  184. data/utils/enveomics/Scripts/lib/enveomics_rb/stats/sample.rb +0 -152
  185. data/utils/enveomics/Scripts/lib/enveomics_rb/stats.rb +0 -3
  186. data/utils/enveomics/Scripts/lib/enveomics_rb/utils.rb +0 -74
  187. data/utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb +0 -135
  188. data/utils/enveomics/Scripts/ogs.annotate.rb +0 -88
  189. data/utils/enveomics/Scripts/ogs.core-pan.rb +0 -160
  190. data/utils/enveomics/Scripts/ogs.extract.rb +0 -125
  191. data/utils/enveomics/Scripts/ogs.mcl.rb +0 -186
  192. data/utils/enveomics/Scripts/ogs.rb +0 -104
  193. data/utils/enveomics/Scripts/ogs.stats.rb +0 -131
  194. data/utils/enveomics/Scripts/rbm-legacy.rb +0 -172
  195. data/utils/enveomics/Scripts/rbm.rb +0 -108
  196. data/utils/enveomics/Scripts/sam.filter.rb +0 -148
  197. data/utils/enveomics/Tests/Makefile +0 -10
  198. data/utils/enveomics/Tests/Mgen_M2288.faa +0 -3189
  199. data/utils/enveomics/Tests/Mgen_M2288.fna +0 -8282
  200. data/utils/enveomics/Tests/Mgen_M2321.fna +0 -8288
  201. data/utils/enveomics/Tests/Nequ_Kin4M.faa +0 -2970
  202. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata +0 -0
  203. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt +0 -7
  204. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv +0 -17
  205. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv +0 -137
  206. data/utils/enveomics/Tests/a_mg.cds-go.blast.tsv +0 -123
  207. data/utils/enveomics/Tests/a_mg.reads-cds.blast.tsv +0 -200
  208. data/utils/enveomics/Tests/a_mg.reads-cds.counts.tsv +0 -55
  209. data/utils/enveomics/Tests/alkB.nwk +0 -1
  210. data/utils/enveomics/Tests/anthrax-cansnp-data.tsv +0 -13
  211. data/utils/enveomics/Tests/anthrax-cansnp-key.tsv +0 -17
  212. data/utils/enveomics/Tests/hiv1.faa +0 -59
  213. data/utils/enveomics/Tests/hiv1.fna +0 -134
  214. data/utils/enveomics/Tests/hiv2.faa +0 -70
  215. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv +0 -233
  216. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim +0 -1
  217. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec +0 -233
  218. data/utils/enveomics/Tests/phyla_counts.tsv +0 -10
  219. data/utils/enveomics/Tests/primate_lentivirus.ogs +0 -11
  220. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm +0 -9
  221. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm +0 -8
  222. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm +0 -6
  223. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm +0 -9
  224. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm +0 -6
  225. data/utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm +0 -6
  226. data/utils/enveomics/build_enveomics_r.bash +0 -45
  227. data/utils/enveomics/enveomics.R/DESCRIPTION +0 -31
  228. data/utils/enveomics/enveomics.R/NAMESPACE +0 -39
  229. data/utils/enveomics/enveomics.R/R/autoprune.R +0 -155
  230. data/utils/enveomics/enveomics.R/R/barplot.R +0 -184
  231. data/utils/enveomics/enveomics.R/R/cliopts.R +0 -135
  232. data/utils/enveomics/enveomics.R/R/df2dist.R +0 -154
  233. data/utils/enveomics/enveomics.R/R/growthcurve.R +0 -331
  234. data/utils/enveomics/enveomics.R/R/prefscore.R +0 -79
  235. data/utils/enveomics/enveomics.R/R/recplot.R +0 -354
  236. data/utils/enveomics/enveomics.R/R/recplot2.R +0 -1631
  237. data/utils/enveomics/enveomics.R/R/tribs.R +0 -583
  238. data/utils/enveomics/enveomics.R/R/utils.R +0 -80
  239. data/utils/enveomics/enveomics.R/README.md +0 -81
  240. data/utils/enveomics/enveomics.R/data/growth.curves.rda +0 -0
  241. data/utils/enveomics/enveomics.R/data/phyla.counts.rda +0 -0
  242. data/utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd +0 -16
  243. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd +0 -16
  244. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd +0 -16
  245. data/utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd +0 -25
  246. data/utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd +0 -46
  247. data/utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd +0 -23
  248. data/utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd +0 -47
  249. data/utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd +0 -23
  250. data/utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd +0 -23
  251. data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd +0 -40
  252. data/utils/enveomics/enveomics.R/man/enve.barplot.Rd +0 -103
  253. data/utils/enveomics/enveomics.R/man/enve.cliopts.Rd +0 -67
  254. data/utils/enveomics/enveomics.R/man/enve.col.alpha.Rd +0 -24
  255. data/utils/enveomics/enveomics.R/man/enve.col2alpha.Rd +0 -19
  256. data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd +0 -45
  257. data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd +0 -44
  258. data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd +0 -47
  259. data/utils/enveomics/enveomics.R/man/enve.growthcurve.Rd +0 -75
  260. data/utils/enveomics/enveomics.R/man/enve.prefscore.Rd +0 -50
  261. data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd +0 -44
  262. data/utils/enveomics/enveomics.R/man/enve.recplot.Rd +0 -139
  263. data/utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd +0 -45
  264. data/utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd +0 -24
  265. data/utils/enveomics/enveomics.R/man/enve.recplot2.Rd +0 -77
  266. data/utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd +0 -25
  267. data/utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd +0 -21
  268. data/utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd +0 -19
  269. data/utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd +0 -19
  270. data/utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd +0 -47
  271. data/utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd +0 -29
  272. data/utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd +0 -18
  273. data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd +0 -45
  274. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd +0 -36
  275. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd +0 -19
  276. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd +0 -19
  277. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd +0 -27
  278. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd +0 -52
  279. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd +0 -17
  280. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd +0 -51
  281. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd +0 -43
  282. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd +0 -82
  283. data/utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd +0 -59
  284. data/utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd +0 -27
  285. data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd +0 -36
  286. data/utils/enveomics/enveomics.R/man/enve.selvector.Rd +0 -23
  287. data/utils/enveomics/enveomics.R/man/enve.tribs.Rd +0 -68
  288. data/utils/enveomics/enveomics.R/man/enve.tribs.test.Rd +0 -28
  289. data/utils/enveomics/enveomics.R/man/enve.truncate.Rd +0 -27
  290. data/utils/enveomics/enveomics.R/man/growth.curves.Rd +0 -14
  291. data/utils/enveomics/enveomics.R/man/phyla.counts.Rd +0 -13
  292. data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd +0 -78
  293. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd +0 -46
  294. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd +0 -45
  295. data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd +0 -125
  296. data/utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd +0 -19
  297. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd +0 -19
  298. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd +0 -19
  299. data/utils/enveomics/globals.mk +0 -8
  300. data/utils/enveomics/manifest.json +0 -9
  301. data/utils/multitrim/Multitrim How-To.pdf +0 -0
  302. data/utils/multitrim/README.md +0 -67
  303. data/utils/multitrim/multitrim.py +0 -1555
  304. data/utils/multitrim/multitrim.yml +0 -13
data/utils/enveomics/Tests/hiv1.faa DELETED
@@ -1,59 +0,0 @@
1
- >lcl|AF033819.3_prot_AAC82593.1_1 [gene=gag] [protein=Gag] [protein_id=AAC82593.1] [location=336..1838]
2
- MGARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQPSLQT
3
- GSEELRSLYNTVATLYCVHQRIEIKDTKEALDKIEEEQNKSKKKAQQAAADTGHSNQVSQNYPIVQNIQG
4
- QMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAA
5
- EWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPT
6
- SILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTAC
7
- QGVGGPGHKARVLAEAMSQVTNSATIMMQRGNFRNQRKIVKCFNCGKEGHTARNCRAPRKKGCWKCGKEG
8
- HQMKDCTERQANFLGKIWPSYKGRPGNFLQSRPEPTAPPEESFRSGVETTTPPQKQEPIDKELYPLTSLR
9
- SLFGNDPSSQ
10
- >lcl|AF033819.3_prot_AAC82598.2_2 [gene=pol] [protein=Pol] [partial=5'] [protein_id=AAC82598.2] [location=<1631..4642]
11
- FFREDLAFLQGKAREFSSEQTRANSPTRRELQVWGRDNNSPSEAGADRQGTVSFNFPQVTLWQRPLVTIK
12
- IGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNI
13
- IGRNLLTQIGCTLNFPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENP
14
- YNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFR
15
- KYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEI
16
- GQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLN
17
- WASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQG
18
- QWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEY
19
- WQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQ
20
- KTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGN
21
- EQVDKLVSAGIRKVLFLDGIDKAQDEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVD
22
- CSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTIHTDNGSNFTGAT
23
- VRAACWWAGIKQEFGIPYNPQSQGVVESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYS
24
- AGERIVDIIATDIQTKELQKQITKIQNFRVYYRDSRNPLWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKA
25
- KIIRDYGKQMAGDDCVASRQDED
26
- >lcl|AF033819.3_prot_AAC82594.1_3 [gene=vif] [protein=Vif] [protein_id=AAC82594.1] [location=4587..5165]
27
- MENRWQVMIVWQVDRMRIRTWKSLVKHHMYVSGKARGWFYRHHYESPHPRISSEVHIPLGDARLVITTYW
28
- GLHTGERDWHLGQGVSIEWRKKRYSTQVDPELADQLIHLYYFDCFSDSAIRKALLGHIVSPRCEYQAGHN
29
- KVGSLQYLALAALITPKKIKPPLPSVTKLTEDRWNKPQKTKGHRGSHTMNGH
30
- >lcl|AF033819.3_prot_AAC82595.1_4 [gene=vpr] [protein=Vpr] [protein_id=AAC82595.1] [location=5105..5341]
31
- MEQAPEDQGPQREPHNEWTLELLEELKNEAVRHFPRIWLHGLGQHIYETYGDTWAGVEAIIRILQQLLFI
32
- HFQNWVST
33
- >lcl|AF033819.3_prot_AAC82591.1_5 [gene=tat] [protein=Tat] [protein_id=AAC82591.1] [location=join(5377..5591,7925..7970)]
34
- MEPVDPRLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFITKALGISYGRKKRRQRRRAHQNSQTHQASLS
35
- KQPTSQPRGDPTGPKE
36
- >lcl|AF033819.3_prot_AAC82592.1_6 [gene=rev] [protein=Rev] [protein_id=AAC82592.1] [location=join(5516..5591,7925..8199)]
37
- MAGRSGDSDEELIRTVRLIKLLYQSNPPPNPEGTRQARRNRRRRWRERQRQIHSISERILGTYLGRSAEP
38
- VPLQLPPLERLTLDCNEDCGTSGTQGVGSPQILVESPTVLESGTKE
39
- >lcl|AF033819.3_prot_AAD20388.1_7 [gene=vpu] [protein=Vpu] [protein_id=AAD20388.1] [location=5608..5856]
40
- MQPIPIVAIVALVVAIIIAIVVWSIVIIEYRKILRQRKIDRLIDRLIERAEDSGNESEGEISALVEMGVE
41
- MGHHAPWDVDDL
42
- >lcl|AF033819.3_prot_AAC82596.1_8 [gene=env] [protein=Env] [protein_id=AAC82596.1] [location=5771..8341]
43
- MRVKEKYQHLWRWGWRWGTMLLGMLMICSATEKLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWA
44
- THACVPTDPNPQEVVLVNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVSLKCTDLKNDTNT
45
- NSSSGRMIMEKGEIKNCSFNISTSIRGKVQKEYAFFYKLDIIPIDNDTTSYKLTSCNTSVITQACPKVSF
46
- EPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSVNFTDN
47
- AKTIIVQLNTSVEINCTRPNNNTRKRIRIQRGPGRAFVTIGKIGNMRQAHCNISRAKWNNTLKQIASKLR
48
- EQFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCNSTQLFNSTWFNSTWSTEGSNNTEGSDTITLPCRI
49
- KQIINMWQKVGKAMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEIFRPGGGDMRDNWRSELYKYKVVK
50
- IEPLGVAPTKAKRRVVQREKRAVGIGALFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQNNLLRAIE
51
- AQQHLLQLTVWGIKQLQARILAVERYLKDQQLLGIWGCSGKLICTTAVPWNASWSNKSLEQIWNHTTWME
52
- WDREINNYTSLIHSLIEESQNQQEKNEQELLELDKWASLWNWFNITNWLWYIKLFIMIVGGLVGLRIVFA
53
- VLSIVNRVRQGYSPLSFQTHLPTPRGPDRPEGIEEEGGERDRDRSIRLVNGSLALIWDDLRSLCLFSYHR
54
- LRDLLLIVTRIVELLGRRGWEALKYWWNLLQYWSQELKNSAVSLLNATAIAVAEGTDRVIEVVQGACRAI
55
- RHIPRRIRQGLERILL
56
- >lcl|AF033819.3_prot_AAC82597.1_9 [gene=nef] [protein=Nef] [protein_id=AAC82597.1] [location=8343..8714]
57
- MGGKWSKSSVIGWPTVRERMRRAEPAADRVGAASRDLEKHGAITSSNTAATNAACAWLEAQEEEEVGFPV
58
- TPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFPD
59
-
data/utils/enveomics/Tests/hiv1.fna DELETED
@@ -1,134 +0,0 @@
1
- >gi|4558520|gb|AF033819.3| HIV-1, complete genome
2
- GGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCC
3
- TCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGA
4
- TCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAA
5
- AGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGG
6
- CGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCG
7
- TCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAAT
8
- ATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGA
9
- AACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTT
10
- AGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGG
11
- AAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACAC
12
- AGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAG
13
- GCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGA
14
- TACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGG
15
- GGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTG
16
- CATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAA
17
- CTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTA
18
- TAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATA
19
- AGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAG
20
- CTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGAC
21
- TATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGA
22
- CCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGC
23
- AGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGC
24
- CAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGAT
25
- TGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTC
26
- TTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCC
27
- CCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAAC
28
- GACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATAC
29
- AGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATC
30
- AAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAG
31
- GACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCAT
32
- TAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCA
33
- TTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAA
34
- AAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAG
35
- AAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCA
36
- CATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTC
37
- CCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGAT
38
- TAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACA
39
- AAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATG
40
- TAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTG
41
- GGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCAT
42
- CCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGA
43
- AGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACT
44
- CCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAA
45
- AACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAA
46
- TACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGG
47
- AAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATA
48
- ACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGG
49
- AAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTT
50
- AGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCA
51
- GCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCC
52
- TAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGA
53
- AGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCA
54
- GAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCAC
55
- ACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTT
56
- AGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGAT
57
- TTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAG
58
- CCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGT
59
- TATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAG
60
- GAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCA
61
- GCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCC
62
- CTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTA
63
- AGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAG
64
- GGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGA
65
- ATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGG
66
- AAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAG
67
- TAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGC
68
- AAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGC
69
- TAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCA
70
- CTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGG
71
- GTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCA
72
- ACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATA
73
- GTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAG
74
- CATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAA
75
- CAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGC
76
- TTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAAC
77
- TTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTT
78
- CAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGA
79
- TCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAA
80
- AAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGC
81
- GGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGT
82
- ACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTT
83
- GTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATA
84
- GACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGG
85
- GGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCAC
86
- AGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCA
87
- TATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAG
88
- TAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGA
89
- TATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAG
90
- TGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGA
91
- TAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTA
92
- TAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTC
93
- ATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTG
94
- CGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATG
95
- TACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTA
96
- GTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAA
97
- TTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATT
98
- TGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAAC
99
- ACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAAT
100
- CCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTC
101
- AACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGA
102
- AGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAA
103
- TGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGA
104
- TGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGA
105
- AGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAA
106
- GAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGG
107
- AAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAG
108
- CAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCA
109
- AGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGG
110
- TTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAA
111
- CAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACT
112
- CCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGC
113
- AAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGA
114
- GGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCAC
115
- CATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGG
116
- TGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTG
117
- CGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAAC
118
- TTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACT
119
- AAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATA
120
- GAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGA
121
- TTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAA
122
- TGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAAT
123
- CACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTG
124
- GGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACT
125
- TTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTG
126
- GATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCA
127
- CTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAG
128
- AGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTG
129
- GAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGC
130
- TGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTG
131
- GGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAG
132
- ACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCC
133
- TTGAGTGCTTC
134
-
data/utils/enveomics/Tests/hiv2.faa DELETED
@@ -1,70 +0,0 @@
1
- >lcl|NC_001722.1_prot_NP_663784.1_1 [gene=gag-pol] [protein=gag-pol fusion polyprotein] [protein_id=NP_663784.1] [location=join(1103..2398,2398..5754)]
2
- MGARNSVLRGKKADELEKVRLRPGGKKKYRLKHIVWAANELDKFGLAESLLESKEGCQKILRVLDPLVPT
3
- GSENLKSLFNTVCVIWCLHAEEKVKDTEEAKKLAQRHLVAETGTAEKMPNTSRPTAPPSGKRGNYPVQQA
4
- GGNYVHVPLSPRTLNAWVKLVEEKKFGAEVVPGFQALSEGCTPYDINQMLNCVGDHQAAMQIIREIINEE
5
- AADWDSQHPIPGPLPAGQLRDPRGSDIAGTTSTVDEQIQWMYRPQNPVPVGNIYRRWIQIGLQKCVRKYN
6
- PTNILDIKQGPKEPFQSYVDRFYKSLRAEQTDPAVKNWMTQTLLIQNANPDCKLVLKGLGMNPTLEEMLT
7
- ACQGVGGPGQKARLMAEALKEAMGPSPIPFAAAQQRKAIRYWNCGKEGHSARQCRAPRRQGCWKCGKPGH
8
- IMANCPERQAGFFRVGPTGKEASQLPRDPSPSGADTNSTSGRSSSGTVGEIYAAREKAEGAEGETIQRGD
9
- GGLAAPRAERDTSQRGDRGLAAPQFSLWKRPVVTAYIEDQPVEVLLDTGADDSIVAGIELGDNYTPKIVG
10
- GIGGFINTKEYKNVEIKVLNKRVRATIMTGDTPINIFGRNILTALGMSLNLPVAKIEPIKVTLKPGKDGP
11
- RLKQWPLTKEKIEALKEICEKMEKEGQLEEAPPTNPYNTPTFAIKKKDKNKWRMLIDFRELNKVTQDFTE
12
- IQLGIPHPAGLAKKKRISILDVGDAYFSIPLHEDFRQYTAFTLPAVNNMEPGKRYIYKVLPQGWKGSPAI
13
- FQYTMRQVLEPFRKANPDVILIQYMDDILIASDRTGLEHDKVVLQLKELLNGLGFSTPDEKFQKDPPFQW
14
- MGCELWPTKWKLQKLQLPQKDIWTVNDIQKLVGVLNWAAQIYSGIKTKHLCRLIRGKMTLTEEVQWTELA
15
- EAELEENKIILSQEQEGYYYQEEKELEATIQKSQGHQWTYKIHQEEKILKVGKYAKIKNTHTNGVRLLAQ
16
- VVQKIGKEALVIWGRIPKFHLPVERETWEQWWDNYWQVTWIPEWDFVSTPPLVRLTFNLVGDPIPGAETF
17
- YTDGSCNRQSKEGKAGYVTDRGKDKVKVLEQTTNQQAELEVFRMALADSGPKVNIIVDSQYVMGIVAGQP
18
- TESENRIVNQIIEEMIKKEAVYVAWVPAHKGIGGNQEVDHLVSQGIRQVLFLEKIEPAQEEHEKYHSIIK
19
- ELTHKFGIPLLVARQIVNSCAQCQQKGEAIHGQVNAEIGVWQMDYTHLEGKIIIVAVHVASGFIEAEVIP
20
- QESGRQTALFLLKLASRWPITHLHTDNGPNFTSQEVKMVAWWVGIEQSFGVPYNPQSQGVVEAMNHHLKN
21
- QISRIREQANTIETIVLMAVHCMNFKRRGGIGDMTPAERLINMITTEQEIQFLQRKNSNFKNFQVYYREG
22
- RDQLWKGPGELLWKGEGAVIVKVGTDIKVVPRRKAKIIRDYGGRQELDSSPHLEGAREDGEMACPCQVPE
23
- IQNKRPRGGALCSPPQGGMGMVDLQQGNIPTTRKKSSRNTGILEPNTRKRMALLSCSKINLVYRKVLDRC
24
- YPRLCRHPNT
25
- >lcl|NC_001722.1_prot_NP_056837.1_2 [gene=gag-pol] [protein=gag polyprotein] [protein_id=NP_056837.1] [location=1103..2668]
26
- MGARNSVLRGKKADELEKVRLRPGGKKKYRLKHIVWAANELDKFGLAESLLESKEGCQKILRVLDPLVPT
27
- GSENLKSLFNTVCVIWCLHAEEKVKDTEEAKKLAQRHLVAETGTAEKMPNTSRPTAPPSGKRGNYPVQQA
28
- GGNYVHVPLSPRTLNAWVKLVEEKKFGAEVVPGFQALSEGCTPYDINQMLNCVGDHQAAMQIIREIINEE
29
- AADWDSQHPIPGPLPAGQLRDPRGSDIAGTTSTVDEQIQWMYRPQNPVPVGNIYRRWIQIGLQKCVRKYN
30
- PTNILDIKQGPKEPFQSYVDRFYKSLRAEQTDPAVKNWMTQTLLIQNANPDCKLVLKGLGMNPTLEEMLT
31
- ACQGVGGPGQKARLMAEALKEAMGPSPIPFAAAQQRKAIRYWNCGKEGHSARQCRAPRRQGCWKCGKPGH
32
- IMANCPERQAGFLGLGPRGKKPRNFPVTQAPQGLIPTAPPADPAAELLERYMQQGRKQREQRERPYKEVT
33
- EDLLHLEQRETPHREETEDLLHLNSLFGKDQ
34
- >lcl|NC_001722.1_prot_NP_056839.1_3 [gene=HIV2gp2] [protein=vif protein] [protein_id=NP_056839.1] [location=5423..6070]
35
- MEEDRNWIVVPTWRVPGRMEKWHALVKYLKYRTKDLEEVRYVPHHKVGWAWWTCSRVIFPLQGKSHLEIQ
36
- AYWNLTPEKGWLSSHAVRLTWYTEKFWTDVTPDCADILIHSTYFSCFTAGEVRRAIRGEKLLSCCNYPQA
37
- HKAQVPSLQYLALVVVQQNDRPQRKGTARKQWRRDHWRGLRVAREDHRSLKQGGSEPSAPRAHFPGVAKV
38
- LEILA
39
- >lcl|NC_001722.1_prot_NP_056840.1_4 [gene=HIV2gp3] [protein=vpx protein] [protein_id=NP_056840.1] [location=5898..6239]
40
- MTDPRERVPPGNSGEETIGEAFEWLERTIEALNREAVNHLPRELIFQVWQRSWRYWHDEQGMSASYTKYR
41
- YLCLMQKAIFTHFKRGCTCWGEDMGREGLEDQGPPPPPPPGLV
42
- >lcl|NC_001722.1_prot_NP_056841.1_5 [gene=HIV2gp4] [protein=vpr protein] [protein_id=NP_056841.1] [location=6239..6502]
43
- MTEAPTEFPPEDGTPRRDLGSDWVIETLREIKEEALRHFDPRLLIALGYYIHNRHGDTLEGARELIKTLQ
44
- RALFVHFRAGCNRSRIG
45
- >lcl|NC_001722.1_prot_NP_056842.1_6 [gene=HIV2gp5] [protein=tat protein] [protein_id=NP_056842.1] [location=join(6402..6697,8861..8957)]
46
- METPLKAPESSLKPYNEPSSCTSERDVTAQELAKQGEELLAQLHRPLEPCTNKCYCKRCSFHCQLCFSKK
47
- GLGISYERKGRRRRTPRKTKTPSPSAPDKSISTRTGDSQPTKEQKKTSEATVVTTCGLGQ
48
- >lcl|NC_001722.1_prot_NP_056843.1_7 [gene=HIV2gp6] [protein=rev protein] [protein_id=NP_056843.1] [location=join(6628..6697,8861..9102)]
49
- MSERADEEGLQGKLRLLRLLHQTNPYPQGPGTASQRRNRRRRRRRQWLRLVALANKLCAVPDPPTDSPLD
50
- RAIQHLQRLTIQELPDPPTDLPESNSNQGLAET
51
- >lcl|NC_001722.1_prot_NP_056844.1_8 [gene=HIV2gp7] [protein=env polyprotein] [protein_id=NP_056844.1] [location=6704..9286]
52
- MEPGRNQLFVVILLTSACLVYCSQYVTVFYGIPAWKNASIPLFCATKNRDTWGTIQCLPDNDDYQEIILN
53
- VTEAFDAWNNTVTEQAVEDVWHLFETSIKPCVKLTPLCVAMNCSRVQGNTTTPNPRTSSSTTSRPPTSAA
54
- SIINETSNCIENNTCAGLGYEEMMQCEFNMKGLEQDKKRRYKDTWYLEDVVCDNTTAGTCYMRHCNTSII
55
- KESCDKHYWDAMRFRYCAPPGFALLRCNDTNYSGFEPKCTKVVAASCTRMMETQTSTWFGFNGTRAENRT
56
- YIYWHGRDNRTIISLNKYYNLTMRCKRPGNKTVLPITLMSGLVFHSQPINTRPRQAWCRFGGRWREAMQE
57
- VKQTLVQHPRYKGINDTGKINFTKPGAGSDPEVAFMWTNCRGEFLYCNMTWFLNWVEDKNQTRRNYCHIK
58
- QIINTWHKVGKNVYLPPREGELACESTVTSIIANIDIDKNRTHTNITFSAEVAELYRLELGDYKLIEITP
59
- IGFAPTDQRRYSSTPVRNKRGVFVLGFLGFLATAGSAMGARSLTLSAQSRTLLAGIVQQQQQLLDVVKRQ
60
- QEMLRLTVWGTKNLQARVTAIEKYLKHQAQLNSWGCAFRQVCHTTVPWVNDSLSPDWKNMTWQEWEKQVR
61
- YLEANISQSLEEAQIQQEKNMYELQKLNSWDILGNWFDLTSWVKYIQYGVHIVVGIIALRIAIYVVQLLS
62
- RFRKGYRPVFSSPPGYLQQIHIHKDRGQPANEGTEEDVGGDSGYDLWPWPINYVQFLIHLLTRLLIGLYN
63
- ICRDLLSKNSPTRRLISQSLTAIRDWLRLKAAQLQYGCEWIQEAFQAFARTTRETLAGAWGWLWEAARRI
64
- GRGILAVPRRIRQGAELALL
65
- >lcl|NC_001722.1_prot_NP_056845.1_9 [gene=HIV2gp8] [protein=nef protein] [protein_id=NP_056845.1] [location=9120..9893]
66
- MGASGSKKLSKHSRGLRERLLRARGDGYGKQRDASGGEYSQFQEESGREQNSPSCEGQQYQQGEYMNSPW
67
- RNPATERQKDLYRQQNMDDVDSDDDDLIGVPVTPRVPRREMTYKLAIDMSHFIKEKGGLQGMFYSRRRHR
68
- ILDIYLEKEEGIIPDWQNYTHGPGVRYPMYFGWLWKLVSVELSQEAEEDEANCLVHPAQTSRHDDEHGET
69
- LVWQFDSMLAYNYKAFTLYPEEFGHKSGLPEKEWKAKLKARGIPYSE
70
-
data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv DELETED
@@ -1,233 +0,0 @@
1
- 2 gi|4558520|gb|AF033819.3| 97.03 101 2 1 1 101 8626 8527 1e-45 169
2
- 3 gi|4558520|gb|AF033819.3| 94.00 100 6 0 1 100 4499 4598 1e-40 152
3
- 6 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 553 652 2e-43 161
4
- 9 gi|4558520|gb|AF033819.3| 93.07 101 5 2 1 100 5662 5563 4e-39 147
5
- 12 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 1541 1640 2e-42 158
6
- 14 gi|4558520|gb|AF033819.3| 94.00 100 6 0 1 100 4742 4841 1e-40 152
7
- 17 gi|4558520|gb|AF033819.3| 94.12 102 4 2 1 102 2564 2663 3e-41 154
8
- 18 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 7821 7722 2e-43 161
9
- 19 gi|4558520|gb|AF033819.3| 94.12 102 4 2 1 102 2559 2460 3e-41 154
10
- 23 gi|4558520|gb|AF033819.3| 96.94 98 1 2 4 100 7816 7912 4e-44 163
11
- 25 gi|4558520|gb|AF033819.3| 96.91 97 3 0 1 97 8552 8648 4e-44 163
12
- 28 gi|4558520|gb|AF033819.3| 96.91 97 3 0 1 97 309 213 4e-44 163
13
- 33 gi|4558520|gb|AF033819.3| 94.12 102 4 2 1 102 2601 2700 3e-41 154
14
- 34 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 2184 2085 1e-45 169
15
- 35 gi|4558520|gb|AF033819.3| 94.00 100 5 1 1 99 3495 3396 3e-40 150
16
- 40 gi|4558520|gb|AF033819.3| 93.94 99 5 1 1 99 1429 1332 1e-39 148
17
- 44 gi|4558520|gb|AF033819.3| 97.03 101 2 1 1 101 6500 6599 1e-45 169
18
- 46 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 771 672 4e-44 163
19
- 47 gi|4558520|gb|AF033819.3| 95.05 101 3 2 1 100 6089 6188 2e-42 158
20
- 48 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 315 414 4e-44 163
21
- 49 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 4928 4829 1e-45 169
22
- 50 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 4023 3924 7e-42 156
23
- 51 gi|4558520|gb|AF033819.3| 95.05 101 3 2 1 100 6570 6471 2e-42 158
24
- 52 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 5494 5395 2e-42 158
25
- 55 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 1056 957 4e-44 163
26
- 56 gi|4558520|gb|AF033819.3| 93.94 99 4 2 1 98 6840 6743 1e-39 148
27
- 58 gi|4558520|gb|AF033819.3| 96.04 101 3 1 1 101 6072 5973 4e-44 163
28
- 60 gi|4558520|gb|AF033819.3| 94.06 101 5 1 1 101 5866 5965 1e-40 152
29
- 63 gi|4558520|gb|AF033819.3| 96.97 99 3 0 1 99 5535 5437 3e-45 167
30
- 65 gi|4558520|gb|AF033819.3| 97.03 101 2 1 1 101 7136 7235 1e-45 169
31
- 66 gi|4558520|gb|AF033819.3| 96.04 101 3 1 1 101 5001 5100 4e-44 163
32
- 68 gi|4558520|gb|AF033819.3| 94.90 98 5 0 1 98 8605 8508 3e-41 154
33
- 70 gi|4558520|gb|AF033819.3| 97.98 99 1 1 1 98 8063 7965 3e-46 171
34
- 71 gi|4558520|gb|AF033819.3| 93.14 102 5 2 1 102 1899 1998 1e-39 148
35
- 72 gi|4558520|gb|AF033819.3| 93.07 101 6 1 1 101 7652 7553 5e-39 147
36
- 73 gi|4558520|gb|AF033819.3| 94.06 101 4 2 1 100 7407 7506 1e-40 152
37
- 75 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 9169 9070 4e-44 163
38
- 75 gi|4558520|gb|AF033819.3| 95.24 84 4 0 1 84 84 1 3e-35 134
39
- 76 gi|4558520|gb|AF033819.3| 96.00 100 2 2 1 98 3393 3294 2e-43 161
40
- 79 gi|4558520|gb|AF033819.3| 94.12 102 3 3 1 101 166 67 1e-40 152
41
- 81 gi|4558520|gb|AF033819.3| 94.00 100 5 1 1 99 2902 3001 3e-40 150
42
- 85 gi|4558520|gb|AF033819.3| 94.00 100 4 2 1 98 7979 8078 3e-40 150
43
- 86 gi|4558520|gb|AF033819.3| 96.00 100 2 2 3 102 3221 3124 2e-43 161
44
- 87 gi|4558520|gb|AF033819.3| 94.06 101 5 1 1 101 8311 8410 1e-40 152
45
- 91 gi|4558520|gb|AF033819.3| 97.92 96 2 0 1 96 3809 3904 3e-45 167
46
- 97 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 8815 8914 7e-42 156
47
- 100 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 3563 3464 2e-42 158
48
- 109 gi|4558520|gb|AF033819.3| 96.04 101 2 2 1 100 6572 6671 4e-44 163
49
- 110 gi|4558520|gb|AF033819.3| 93.20 103 4 3 1 102 7432 7532 1e-39 148
50
- 112 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 8628 8529 7e-42 156
51
- 113 gi|4558520|gb|AF033819.3| 94.85 97 3 2 1 96 1001 1096 3e-40 150
52
- 114 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 207 108 7e-42 156
53
- 116 gi|4558520|gb|AF033819.3| 95.96 99 4 0 1 99 4408 4310 2e-43 161
54
- 117 gi|4558520|gb|AF033819.3| 96.91 97 2 1 3 98 2591 2687 2e-43 161
55
- 122 gi|4558520|gb|AF033819.3| 94.06 101 5 1 1 101 4430 4529 1e-40 152
56
- 123 gi|4558520|gb|AF033819.3| 96.91 97 3 0 1 97 6771 6867 4e-44 163
57
- 125 gi|4558520|gb|AF033819.3| 94.00 100 5 1 1 99 868 967 3e-40 150
58
- 126 gi|4558520|gb|AF033819.3| 98.00 100 2 0 1 100 8524 8623 2e-47 174
59
- 127 gi|4558520|gb|AF033819.3| 93.88 98 6 0 1 98 4858 4761 1e-39 148
60
- 128 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 3091 3190 1e-45 169
61
- 132 gi|4558520|gb|AF033819.3| 97.96 98 2 0 1 98 2864 2767 3e-46 171
62
- 138 gi|4558520|gb|AF033819.3| 94.00 100 5 1 1 99 3780 3879 3e-40 150
63
- 143 gi|4558520|gb|AF033819.3| 95.88 97 4 0 1 97 389 485 2e-42 158
64
- 147 gi|4558520|gb|AF033819.3| 94.90 98 5 0 1 98 7601 7698 3e-41 154
65
- 148 gi|4558520|gb|AF033819.3| 93.00 100 6 1 1 99 4224 4125 2e-38 145
66
- 151 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 7072 6973 1e-45 169
67
- 152 gi|4558520|gb|AF033819.3| 97.94 97 2 0 1 97 871 967 1e-45 169
68
- 153 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 6419 6320 2e-42 158
69
- 157 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 7988 7889 4e-44 163
70
- 159 gi|4558520|gb|AF033819.3| 97.98 99 2 0 1 99 7249 7347 7e-47 172
71
- 164 gi|4558520|gb|AF033819.3| 93.14 102 5 2 1 102 6862 6961 1e-39 148
72
- 165 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 4350 4251 2e-43 161
73
- 166 gi|4558520|gb|AF033819.3| 94.00 100 6 0 1 100 5519 5420 1e-40 152
74
- 167 gi|4558520|gb|AF033819.3| 94.00 100 4 2 1 98 1996 2095 3e-40 150
75
- 168 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 6319 6220 7e-42 156
76
- 169 gi|4558520|gb|AF033819.3| 99.00 100 0 1 1 99 4211 4310 2e-48 178
77
- 170 gi|4558520|gb|AF033819.3| 95.05 101 3 2 1 101 258 160 2e-42 158
78
- 172 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 1835 1934 2e-43 161
79
- 173 gi|4558520|gb|AF033819.3| 93.00 100 7 0 1 100 4744 4645 4e-39 147
80
- 175 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 2245 2344 7e-42 156
81
- 177 gi|4558520|gb|AF033819.3| 92.08 101 7 1 1 101 4239 4140 2e-37 141
82
- 181 gi|4558520|gb|AF033819.3| 94.12 102 2 4 1 100 7812 7713 1e-40 152
83
- 185 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 2859 2760 7e-42 156
84
- 189 gi|4558520|gb|AF033819.3| 96.00 100 2 2 1 98 2328 2427 2e-43 161
85
- 191 gi|4558520|gb|AF033819.3| 94.00 100 6 0 1 100 1049 950 1e-40 152
86
- 193 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 6925 7024 2e-42 158
87
- 195 gi|4558520|gb|AF033819.3| 92.00 100 6 2 1 99 3189 3091 7e-37 139
88
- 196 gi|4558520|gb|AF033819.3| 94.00 100 5 1 1 99 7156 7057 3e-40 150
89
- 198 gi|4558520|gb|AF033819.3| 95.00 100 3 2 1 98 8894 8993 7e-42 156
90
- 199 gi|4558520|gb|AF033819.3| 95.05 101 2 3 1 99 5526 5427 7e-42 156
91
- 200 gi|4558520|gb|AF033819.3| 94.00 100 5 1 1 99 6101 6002 3e-40 150
92
- 205 gi|4558520|gb|AF033819.3| 96.91 97 3 0 1 97 799 703 4e-44 163
93
- 206 gi|4558520|gb|AF033819.3| 96.08 102 2 2 1 102 6278 6179 1e-44 165
94
- 207 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 1539 1440 4e-44 163
95
- 210 gi|4558520|gb|AF033819.3| 94.00 100 5 1 1 100 4363 4461 3e-40 150
96
- 211 gi|4558520|gb|AF033819.3| 95.05 101 3 2 1 100 3274 3373 2e-42 158
97
- 213 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 2528 2429 1e-45 169
98
- 215 gi|4558520|gb|AF033819.3| 95.05 101 3 2 1 100 2692 2593 2e-42 158
99
- 217 gi|4558520|gb|AF033819.3| 97.00 100 2 1 1 99 3875 3974 3e-45 167
100
- 219 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 1301 1202 2e-43 161
101
- 221 gi|4558520|gb|AF033819.3| 98.00 100 2 0 1 100 2219 2318 2e-47 174
102
- 223 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 9052 9151 7e-42 156
103
- 223 gi|4558520|gb|AF033819.3| 93.94 66 3 1 35 99 1 66 1e-24 99.0
104
- 225 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 5238 5337 2e-42 158
105
- 228 gi|4558520|gb|AF033819.3| 94.06 101 5 1 1 101 2779 2878 1e-40 152
106
- 230 gi|4558520|gb|AF033819.3| 92.93 99 7 0 1 99 422 520 2e-38 145
107
- 231 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 272 371 2e-42 158
108
- 233 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 4096 4195 2e-42 158
109
- 234 gi|4558520|gb|AF033819.3| 93.00 100 7 0 1 100 7223 7322 4e-39 147
110
- 237 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 8572 8473 1e-45 169
111
- 238 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 5713 5614 4e-44 163
112
- 239 gi|4558520|gb|AF033819.3| 95.88 97 4 0 1 97 8899 8803 2e-42 158
113
- 240 gi|4558520|gb|AF033819.3| 95.05 101 4 1 1 101 6817 6718 2e-42 158
114
- 242 gi|4558520|gb|AF033819.3| 94.85 97 3 2 1 95 5361 5457 3e-40 150
115
- 251 gi|4558520|gb|AF033819.3| 94.06 101 5 1 1 101 865 964 1e-40 152
116
- 253 gi|4558520|gb|AF033819.3| 92.00 100 7 1 1 99 8540 8441 7e-37 139
117
- 254 gi|4558520|gb|AF033819.3| 94.06 101 5 1 1 101 7072 7171 1e-40 152
118
- 255 gi|4558520|gb|AF033819.3| 91.00 100 9 0 1 100 1579 1678 1e-35 135
119
- 256 gi|4558520|gb|AF033819.3| 95.92 98 3 1 1 97 4699 4602 2e-42 158
120
- 260 gi|4558520|gb|AF033819.3| 97.00 100 2 1 1 99 617 518 3e-45 167
121
- 261 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 3212 3311 1e-45 169
122
- 264 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 9066 8967 4e-44 163
123
- 270 gi|4558520|gb|AF033819.3| 97.94 97 2 0 1 97 6604 6508 9e-46 169
124
- 271 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 7747 7648 2e-43 161
125
- 273 gi|4558520|gb|AF033819.3| 93.27 104 3 4 1 104 8331 8430 4e-40 150
126
- 274 gi|4558520|gb|AF033819.3| 94.06 101 4 2 1 100 7707 7806 1e-40 152
127
- 275 gi|4558520|gb|AF033819.3| 97.00 100 2 1 1 99 6754 6853 3e-45 167
128
- 277 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 8802 8703 1e-45 169
129
- 278 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 5040 4941 2e-43 161
130
- 280 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 925 1024 2e-43 161
131
- 284 gi|4558520|gb|AF033819.3| 94.06 101 4 2 1 100 212 311 1e-40 152
132
- 285 gi|4558520|gb|AF033819.3| 96.94 98 3 0 1 98 5882 5979 1e-44 165
133
- 287 gi|4558520|gb|AF033819.3| 93.07 101 5 2 1 100 3426 3525 4e-39 147
134
- 288 gi|4558520|gb|AF033819.3| 97.03 101 2 1 1 101 6897 6996 1e-45 169
135
- 290 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 492 591 2e-42 158
136
- 295 gi|4558520|gb|AF033819.3| 94.95 99 4 1 3 101 5246 5343 3e-41 154
137
- 297 gi|4558520|gb|AF033819.3| 96.04 101 3 1 1 101 1240 1141 4e-44 163
138
- 298 gi|4558520|gb|AF033819.3| 97.00 100 2 1 1 100 934 836 3e-45 167
139
- 301 gi|4558520|gb|AF033819.3| 93.00 100 6 1 1 99 5086 5185 2e-38 145
140
- 302 gi|4558520|gb|AF033819.3| 94.90 98 4 1 4 101 9114 9018 1e-40 152
141
- 303 gi|4558520|gb|AF033819.3| 96.88 96 2 1 1 96 8526 8620 6e-43 159
142
- 305 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 9066 9165 7e-42 156
143
- 305 gi|4558520|gb|AF033819.3| 95.00 80 3 1 21 99 1 80 2e-32 124
144
- 307 gi|4558520|gb|AF033819.3| 94.00 100 6 0 1 100 3263 3164 1e-40 152
145
- 313 gi|4558520|gb|AF033819.3| 95.05 101 4 1 1 101 2302 2401 2e-42 158
146
- 315 gi|4558520|gb|AF033819.3| 94.00 100 5 1 1 99 6651 6552 3e-40 150
147
- 316 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 4702 4801 4e-44 163
148
- 319 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 5363 5462 4e-44 163
149
- 320 gi|4558520|gb|AF033819.3| 97.98 99 2 0 1 99 4305 4403 7e-47 172
150
- 321 gi|4558520|gb|AF033819.3| 95.05 101 4 1 1 101 2970 3069 2e-42 158
151
- 322 gi|4558520|gb|AF033819.3| 97.03 101 2 1 1 101 3651 3750 1e-45 169
152
- 323 gi|4558520|gb|AF033819.3| 93.00 100 5 2 1 98 9070 8971 2e-38 145
153
- 325 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 7301 7400 2e-43 161
154
- 326 gi|4558520|gb|AF033819.3| 94.06 101 3 3 1 99 1641 1542 3e-40 150
155
- 332 gi|4558520|gb|AF033819.3| 98.00 100 2 0 1 100 6132 6033 2e-47 174
156
- 333 gi|4558520|gb|AF033819.3| 93.48 92 5 1 1 91 5053 4962 1e-35 135
157
- 335 gi|4558520|gb|AF033819.3| 94.06 101 5 1 1 101 5201 5102 1e-40 152
158
- 336 gi|4558520|gb|AF033819.3| 92.71 96 7 0 2 97 1001 1096 8e-37 139
159
- 338 gi|4558520|gb|AF033819.3| 93.14 102 5 2 1 102 3105 3006 1e-39 148
160
- 339 gi|4558520|gb|AF033819.3| 95.92 98 3 1 1 97 5754 5657 2e-42 158
161
- 342 gi|4558520|gb|AF033819.3| 94.06 101 5 1 1 101 829 928 1e-40 152
162
- 343 gi|4558520|gb|AF033819.3| 93.07 101 5 2 1 100 7077 6978 4e-39 147
163
- 344 gi|4558520|gb|AF033819.3| 94.06 101 4 2 1 100 3925 4024 1e-40 152
164
- 345 gi|4558520|gb|AF033819.3| 95.96 99 3 1 1 98 2046 2144 6e-43 159
165
- 353 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 7951 8050 2e-42 158
166
- 354 gi|4558520|gb|AF033819.3| 96.81 94 3 0 1 94 9110 9017 2e-42 158
167
- 355 gi|4558520|gb|AF033819.3| 91.09 101 8 1 1 101 5507 5606 1e-35 135
168
- 362 gi|4558520|gb|AF033819.3| 93.07 101 5 2 1 100 5709 5808 4e-39 147
169
- 363 gi|4558520|gb|AF033819.3| 94.00 100 6 0 1 100 6394 6295 1e-40 152
170
- 368 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 6553 6652 1e-45 169
171
- 369 gi|4558520|gb|AF033819.3| 98.00 100 2 0 1 100 7296 7395 2e-47 174
172
- 370 gi|4558520|gb|AF033819.3| 96.00 100 3 1 3 102 30 128 2e-43 161
173
- 370 gi|4558520|gb|AF033819.3| 95.59 68 2 1 3 70 9115 9181 2e-27 108
174
- 371 gi|4558520|gb|AF033819.3| 93.00 100 7 0 1 100 6786 6687 4e-39 147
175
- 372 gi|4558520|gb|AF033819.3| 96.04 101 3 1 1 101 5867 5768 4e-44 163
176
- 376 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 5460 5559 4e-44 163
177
- 377 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 1437 1536 2e-43 161
178
- 380 gi|4558520|gb|AF033819.3| 97.00 100 2 1 1 99 3968 3869 3e-45 167
179
- 385 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 6936 7035 2e-42 158
180
- 387 gi|4558520|gb|AF033819.3| 96.94 98 1 2 1 97 1860 1764 4e-44 163
181
- 388 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 7149 7248 2e-42 158
182
- 389 gi|4558520|gb|AF033819.3| 97.94 97 2 0 1 97 6961 6865 1e-45 169
183
- 393 gi|4558520|gb|AF033819.3| 94.06 101 5 1 1 101 677 776 1e-40 152
184
- 396 gi|4558520|gb|AF033819.3| 95.00 100 3 2 1 98 2539 2440 7e-42 156
185
- 404 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 5732 5633 7e-42 156
186
- 405 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 5455 5554 2e-43 161
187
- 407 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 6462 6561 2e-42 158
188
- 408 gi|4558520|gb|AF033819.3| 95.05 101 4 1 1 101 220 121 2e-42 158
189
- 412 gi|4558520|gb|AF033819.3| 94.00 100 6 0 1 100 4617 4518 1e-40 152
190
- 413 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 3678 3777 2e-42 158
191
- 416 gi|4558520|gb|AF033819.3| 94.00 100 6 0 1 100 8724 8625 1e-40 152
192
- 417 gi|4558520|gb|AF033819.3| 93.00 100 7 0 1 100 6576 6675 4e-39 147
193
- 418 gi|4558520|gb|AF033819.3| 95.88 97 3 1 1 96 8638 8542 7e-42 156
194
- 420 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 8851 8752 2e-43 161
195
- 421 gi|4558520|gb|AF033819.3| 93.07 101 6 1 1 101 2322 2223 5e-39 147
196
- 422 gi|4558520|gb|AF033819.3| 93.00 100 6 1 1 99 6743 6644 2e-38 145
197
- 425 gi|4558520|gb|AF033819.3| 92.00 100 7 1 1 99 3990 3891 7e-37 139
198
- 426 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 3598 3697 1e-45 169
199
- 428 gi|4558520|gb|AF033819.3| 96.04 101 4 0 1 101 1407 1507 1e-44 165
200
- 429 gi|4558520|gb|AF033819.3| 97.00 100 1 2 1 98 3439 3340 3e-45 167
201
- 436 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 8315 8414 7e-42 156
202
- 438 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 1808 1907 4e-44 163
203
- 439 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 7868 7769 1e-45 169
204
- 440 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 7249 7348 1e-45 169
205
- 441 gi|4558520|gb|AF033819.3| 93.94 99 6 0 1 99 5687 5589 3e-40 150
206
- 443 gi|4558520|gb|AF033819.3| 98.02 101 1 1 1 101 8474 8573 2e-47 174
207
- 446 gi|4558520|gb|AF033819.3| 95.96 99 4 0 1 99 2138 2236 2e-43 161
208
- 448 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 4172 4073 2e-42 158
209
- 450 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 100 5366 5268 7e-42 156
210
- 451 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 7335 7236 2e-43 161
211
- 454 gi|4558520|gb|AF033819.3| 94.06 101 4 2 1 101 2460 2558 1e-40 152
212
- 455 gi|4558520|gb|AF033819.3| 95.05 101 4 1 1 101 1266 1167 2e-42 158
213
- 457 gi|4558520|gb|AF033819.3| 95.88 97 3 1 1 97 3177 3082 7e-42 156
214
- 463 gi|4558520|gb|AF033819.3| 99.00 100 1 0 1 100 5227 5128 4e-49 180
215
- 464 gi|4558520|gb|AF033819.3| 96.84 95 3 0 1 95 8589 8683 6e-43 159
216
- 465 gi|4558520|gb|AF033819.3| 93.20 103 4 3 1 103 2775 2676 1e-39 148
217
- 466 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 8430 8331 7e-42 156
218
- 470 gi|4558520|gb|AF033819.3| 96.04 101 3 1 1 101 7790 7691 4e-44 163
219
- 471 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 149 50 2e-42 158
220
- 472 gi|4558520|gb|AF033819.3| 98.00 100 1 1 1 99 1495 1396 7e-47 172
221
- 475 gi|4558520|gb|AF033819.3| 94.00 100 6 0 1 100 140 41 1e-40 152
222
- 476 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 2215 2116 2e-43 161
223
- 482 gi|4558520|gb|AF033819.3| 93.94 99 3 3 1 96 5480 5578 4e-39 147
224
- 485 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 7907 7808 2e-42 158
225
- 486 gi|4558520|gb|AF033819.3| 94.00 100 3 3 1 98 4990 5088 1e-39 148
226
- 487 gi|4558520|gb|AF033819.3| 97.00 100 2 1 1 99 9157 9058 3e-45 167
227
- 487 gi|4558520|gb|AF033819.3| 95.83 72 2 1 1 71 72 1 1e-29 115
228
- 488 gi|4558520|gb|AF033819.3| 95.10 102 2 3 1 101 231 132 2e-42 158
229
- 490 gi|4558520|gb|AF033819.3| 95.10 102 3 2 1 102 7064 6965 6e-43 159
230
- 492 gi|4558520|gb|AF033819.3| 96.84 95 2 1 1 94 6389 6295 2e-42 158
231
- 495 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 4727 4826 1e-45 169
232
- 498 gi|4558520|gb|AF033819.3| 96.08 102 2 1 1 102 4303 4204 1e-44 165
233
- 499 gi|4558520|gb|AF033819.3| 98.00 100 1 1 1 99 6832 6931 7e-47 172
data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim DELETED
@@ -1 +0,0 @@
1
- gi|4558520|gb|AF033819.3| 1 9182