miga-base 1.2.15.1 → 1.2.15.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (305) 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 +44 -8
  6. data/lib/miga/taxonomy.rb +6 -0
  7. data/lib/miga/version.rb +2 -2
  8. data/test/remote_dataset_test.rb +3 -1
  9. metadata +6 -302
  10. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Archaea_SCG.hmm +0 -41964
  11. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Bacteria_SCG.hmm +0 -32439
  12. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Complete_SCG_DB.hmm +0 -62056
  13. data/utils/FastAAI/FastAAI +0 -3659
  14. data/utils/FastAAI/FastAAI-legacy/FastAAI +0 -1336
  15. data/utils/FastAAI/FastAAI-legacy/kAAI_v1.0_virus.py +0 -1296
  16. data/utils/FastAAI/README.md +0 -84
  17. data/utils/enveomics/Docs/recplot2.md +0 -244
  18. data/utils/enveomics/Examples/aai-matrix.bash +0 -66
  19. data/utils/enveomics/Examples/ani-matrix.bash +0 -66
  20. data/utils/enveomics/Examples/essential-phylogeny.bash +0 -105
  21. data/utils/enveomics/Examples/unus-genome-phylogeny.bash +0 -100
  22. data/utils/enveomics/LICENSE.txt +0 -73
  23. data/utils/enveomics/Makefile +0 -52
  24. data/utils/enveomics/Manifest/Tasks/aasubs.json +0 -103
  25. data/utils/enveomics/Manifest/Tasks/blasttab.json +0 -790
  26. data/utils/enveomics/Manifest/Tasks/distances.json +0 -161
  27. data/utils/enveomics/Manifest/Tasks/fasta.json +0 -802
  28. data/utils/enveomics/Manifest/Tasks/fastq.json +0 -291
  29. data/utils/enveomics/Manifest/Tasks/graphics.json +0 -126
  30. data/utils/enveomics/Manifest/Tasks/mapping.json +0 -137
  31. data/utils/enveomics/Manifest/Tasks/ogs.json +0 -382
  32. data/utils/enveomics/Manifest/Tasks/other.json +0 -906
  33. data/utils/enveomics/Manifest/Tasks/remote.json +0 -355
  34. data/utils/enveomics/Manifest/Tasks/sequence-identity.json +0 -650
  35. data/utils/enveomics/Manifest/Tasks/tables.json +0 -308
  36. data/utils/enveomics/Manifest/Tasks/trees.json +0 -68
  37. data/utils/enveomics/Manifest/Tasks/variants.json +0 -111
  38. data/utils/enveomics/Manifest/categories.json +0 -165
  39. data/utils/enveomics/Manifest/examples.json +0 -162
  40. data/utils/enveomics/Manifest/tasks.json +0 -4
  41. data/utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash +0 -69
  42. data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +0 -1
  43. data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +0 -1
  44. data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +0 -1
  45. data/utils/enveomics/Pipelines/assembly.pbs/README.md +0 -189
  46. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash +0 -112
  47. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash +0 -23
  48. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash +0 -44
  49. data/utils/enveomics/Pipelines/assembly.pbs/RUNME.bash +0 -50
  50. data/utils/enveomics/Pipelines/assembly.pbs/kSelector.R +0 -37
  51. data/utils/enveomics/Pipelines/assembly.pbs/newbler.pbs +0 -68
  52. data/utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl +0 -49
  53. data/utils/enveomics/Pipelines/assembly.pbs/soap.pbs +0 -80
  54. data/utils/enveomics/Pipelines/assembly.pbs/stats.pbs +0 -57
  55. data/utils/enveomics/Pipelines/assembly.pbs/velvet.pbs +0 -63
  56. data/utils/enveomics/Pipelines/blast.pbs/01.pbs.bash +0 -38
  57. data/utils/enveomics/Pipelines/blast.pbs/02.pbs.bash +0 -73
  58. data/utils/enveomics/Pipelines/blast.pbs/03.pbs.bash +0 -21
  59. data/utils/enveomics/Pipelines/blast.pbs/BlastTab.recover_job.pl +0 -72
  60. data/utils/enveomics/Pipelines/blast.pbs/CONFIG.mock.bash +0 -98
  61. data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +0 -1
  62. data/utils/enveomics/Pipelines/blast.pbs/README.md +0 -127
  63. data/utils/enveomics/Pipelines/blast.pbs/RUNME.bash +0 -109
  64. data/utils/enveomics/Pipelines/blast.pbs/TASK.check.bash +0 -128
  65. data/utils/enveomics/Pipelines/blast.pbs/TASK.dry.bash +0 -16
  66. data/utils/enveomics/Pipelines/blast.pbs/TASK.eo.bash +0 -22
  67. data/utils/enveomics/Pipelines/blast.pbs/TASK.pause.bash +0 -26
  68. data/utils/enveomics/Pipelines/blast.pbs/TASK.run.bash +0 -89
  69. data/utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash +0 -29
  70. data/utils/enveomics/Pipelines/idba.pbs/README.md +0 -49
  71. data/utils/enveomics/Pipelines/idba.pbs/RUNME.bash +0 -95
  72. data/utils/enveomics/Pipelines/idba.pbs/run.pbs +0 -56
  73. data/utils/enveomics/Pipelines/trim.pbs/README.md +0 -54
  74. data/utils/enveomics/Pipelines/trim.pbs/RUNME.bash +0 -70
  75. data/utils/enveomics/Pipelines/trim.pbs/run.pbs +0 -130
  76. data/utils/enveomics/README.md +0 -42
  77. data/utils/enveomics/Scripts/AAsubs.log2ratio.rb +0 -171
  78. data/utils/enveomics/Scripts/Aln.cat.rb +0 -221
  79. data/utils/enveomics/Scripts/Aln.convert.pl +0 -35
  80. data/utils/enveomics/Scripts/AlphaDiversity.pl +0 -152
  81. data/utils/enveomics/Scripts/BedGraph.tad.rb +0 -93
  82. data/utils/enveomics/Scripts/BedGraph.window.rb +0 -71
  83. data/utils/enveomics/Scripts/BlastPairwise.AAsubs.pl +0 -102
  84. data/utils/enveomics/Scripts/BlastTab.addlen.rb +0 -63
  85. data/utils/enveomics/Scripts/BlastTab.advance.bash +0 -48
  86. data/utils/enveomics/Scripts/BlastTab.best_hit_sorted.pl +0 -55
  87. data/utils/enveomics/Scripts/BlastTab.catsbj.pl +0 -104
  88. data/utils/enveomics/Scripts/BlastTab.cogCat.rb +0 -76
  89. data/utils/enveomics/Scripts/BlastTab.filter.pl +0 -47
  90. data/utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl +0 -194
  91. data/utils/enveomics/Scripts/BlastTab.metaxaPrep.pl +0 -104
  92. data/utils/enveomics/Scripts/BlastTab.pairedHits.rb +0 -157
  93. data/utils/enveomics/Scripts/BlastTab.recplot2.R +0 -48
  94. data/utils/enveomics/Scripts/BlastTab.seqdepth.pl +0 -86
  95. data/utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl +0 -119
  96. data/utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl +0 -86
  97. data/utils/enveomics/Scripts/BlastTab.subsample.pl +0 -47
  98. data/utils/enveomics/Scripts/BlastTab.sumPerHit.pl +0 -114
  99. data/utils/enveomics/Scripts/BlastTab.taxid2taxrank.pl +0 -90
  100. data/utils/enveomics/Scripts/BlastTab.topHits_sorted.rb +0 -123
  101. data/utils/enveomics/Scripts/Chao1.pl +0 -97
  102. data/utils/enveomics/Scripts/CharTable.classify.rb +0 -234
  103. data/utils/enveomics/Scripts/EBIseq2tax.rb +0 -83
  104. data/utils/enveomics/Scripts/FastA.N50.pl +0 -60
  105. data/utils/enveomics/Scripts/FastA.extract.rb +0 -152
  106. data/utils/enveomics/Scripts/FastA.filter.pl +0 -52
  107. data/utils/enveomics/Scripts/FastA.filterLen.pl +0 -28
  108. data/utils/enveomics/Scripts/FastA.filterN.pl +0 -60
  109. data/utils/enveomics/Scripts/FastA.fragment.rb +0 -100
  110. data/utils/enveomics/Scripts/FastA.gc.pl +0 -42
  111. data/utils/enveomics/Scripts/FastA.interpose.pl +0 -93
  112. data/utils/enveomics/Scripts/FastA.length.pl +0 -38
  113. data/utils/enveomics/Scripts/FastA.mask.rb +0 -89
  114. data/utils/enveomics/Scripts/FastA.per_file.pl +0 -36
  115. data/utils/enveomics/Scripts/FastA.qlen.pl +0 -57
  116. data/utils/enveomics/Scripts/FastA.rename.pl +0 -65
  117. data/utils/enveomics/Scripts/FastA.revcom.pl +0 -23
  118. data/utils/enveomics/Scripts/FastA.sample.rb +0 -98
  119. data/utils/enveomics/Scripts/FastA.slider.pl +0 -85
  120. data/utils/enveomics/Scripts/FastA.split.pl +0 -55
  121. data/utils/enveomics/Scripts/FastA.split.rb +0 -79
  122. data/utils/enveomics/Scripts/FastA.subsample.pl +0 -131
  123. data/utils/enveomics/Scripts/FastA.tag.rb +0 -65
  124. data/utils/enveomics/Scripts/FastA.toFastQ.rb +0 -69
  125. data/utils/enveomics/Scripts/FastA.wrap.rb +0 -48
  126. data/utils/enveomics/Scripts/FastQ.filter.pl +0 -54
  127. data/utils/enveomics/Scripts/FastQ.interpose.pl +0 -90
  128. data/utils/enveomics/Scripts/FastQ.maskQual.rb +0 -89
  129. data/utils/enveomics/Scripts/FastQ.offset.pl +0 -90
  130. data/utils/enveomics/Scripts/FastQ.split.pl +0 -53
  131. data/utils/enveomics/Scripts/FastQ.tag.rb +0 -70
  132. data/utils/enveomics/Scripts/FastQ.test-error.rb +0 -81
  133. data/utils/enveomics/Scripts/FastQ.toFastA.awk +0 -24
  134. data/utils/enveomics/Scripts/GFF.catsbj.pl +0 -127
  135. data/utils/enveomics/Scripts/GenBank.add_fields.rb +0 -84
  136. data/utils/enveomics/Scripts/HMM.essential.rb +0 -351
  137. data/utils/enveomics/Scripts/HMM.haai.rb +0 -168
  138. data/utils/enveomics/Scripts/HMMsearch.extractIds.rb +0 -83
  139. data/utils/enveomics/Scripts/JPlace.distances.rb +0 -88
  140. data/utils/enveomics/Scripts/JPlace.to_iToL.rb +0 -320
  141. data/utils/enveomics/Scripts/M5nr.getSequences.rb +0 -81
  142. data/utils/enveomics/Scripts/MeTaxa.distribution.pl +0 -198
  143. data/utils/enveomics/Scripts/MyTaxa.fragsByTax.pl +0 -35
  144. data/utils/enveomics/Scripts/MyTaxa.seq-taxrank.rb +0 -49
  145. data/utils/enveomics/Scripts/NCBIacc2tax.rb +0 -92
  146. data/utils/enveomics/Scripts/Newick.autoprune.R +0 -27
  147. data/utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl +0 -228
  148. data/utils/enveomics/Scripts/RecPlot2.compareIdentities.R +0 -32
  149. data/utils/enveomics/Scripts/RefSeq.download.bash +0 -48
  150. data/utils/enveomics/Scripts/SRA.download.bash +0 -55
  151. data/utils/enveomics/Scripts/TRIBS.plot-test.R +0 -36
  152. data/utils/enveomics/Scripts/TRIBS.test.R +0 -39
  153. data/utils/enveomics/Scripts/Table.barplot.R +0 -31
  154. data/utils/enveomics/Scripts/Table.df2dist.R +0 -30
  155. data/utils/enveomics/Scripts/Table.filter.pl +0 -61
  156. data/utils/enveomics/Scripts/Table.merge.pl +0 -77
  157. data/utils/enveomics/Scripts/Table.prefScore.R +0 -60
  158. data/utils/enveomics/Scripts/Table.replace.rb +0 -69
  159. data/utils/enveomics/Scripts/Table.round.rb +0 -63
  160. data/utils/enveomics/Scripts/Table.split.pl +0 -57
  161. data/utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb +0 -227
  162. data/utils/enveomics/Scripts/VCF.KaKs.rb +0 -147
  163. data/utils/enveomics/Scripts/VCF.SNPs.rb +0 -88
  164. data/utils/enveomics/Scripts/aai.rb +0 -421
  165. data/utils/enveomics/Scripts/ani.rb +0 -362
  166. data/utils/enveomics/Scripts/anir.rb +0 -137
  167. data/utils/enveomics/Scripts/clust.rand.rb +0 -102
  168. data/utils/enveomics/Scripts/gi2tax.rb +0 -103
  169. data/utils/enveomics/Scripts/in_silico_GA_GI.pl +0 -96
  170. data/utils/enveomics/Scripts/lib/data/dupont_2012_essential.hmm.gz +0 -0
  171. data/utils/enveomics/Scripts/lib/data/lee_2019_essential.hmm.gz +0 -0
  172. data/utils/enveomics/Scripts/lib/enveomics.R +0 -1
  173. data/utils/enveomics/Scripts/lib/enveomics_rb/anir.rb +0 -293
  174. data/utils/enveomics/Scripts/lib/enveomics_rb/bm_set.rb +0 -175
  175. data/utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb +0 -24
  176. data/utils/enveomics/Scripts/lib/enveomics_rb/errors.rb +0 -17
  177. data/utils/enveomics/Scripts/lib/enveomics_rb/gmm_em.rb +0 -30
  178. data/utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb +0 -253
  179. data/utils/enveomics/Scripts/lib/enveomics_rb/match.rb +0 -88
  180. data/utils/enveomics/Scripts/lib/enveomics_rb/og.rb +0 -182
  181. data/utils/enveomics/Scripts/lib/enveomics_rb/rbm.rb +0 -49
  182. data/utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb +0 -74
  183. data/utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb +0 -237
  184. data/utils/enveomics/Scripts/lib/enveomics_rb/stats/rand.rb +0 -31
  185. data/utils/enveomics/Scripts/lib/enveomics_rb/stats/sample.rb +0 -152
  186. data/utils/enveomics/Scripts/lib/enveomics_rb/stats.rb +0 -3
  187. data/utils/enveomics/Scripts/lib/enveomics_rb/utils.rb +0 -74
  188. data/utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb +0 -135
  189. data/utils/enveomics/Scripts/ogs.annotate.rb +0 -88
  190. data/utils/enveomics/Scripts/ogs.core-pan.rb +0 -160
  191. data/utils/enveomics/Scripts/ogs.extract.rb +0 -125
  192. data/utils/enveomics/Scripts/ogs.mcl.rb +0 -186
  193. data/utils/enveomics/Scripts/ogs.rb +0 -104
  194. data/utils/enveomics/Scripts/ogs.stats.rb +0 -131
  195. data/utils/enveomics/Scripts/rbm-legacy.rb +0 -172
  196. data/utils/enveomics/Scripts/rbm.rb +0 -108
  197. data/utils/enveomics/Scripts/sam.filter.rb +0 -148
  198. data/utils/enveomics/Tests/Makefile +0 -10
  199. data/utils/enveomics/Tests/Mgen_M2288.faa +0 -3189
  200. data/utils/enveomics/Tests/Mgen_M2288.fna +0 -8282
  201. data/utils/enveomics/Tests/Mgen_M2321.fna +0 -8288
  202. data/utils/enveomics/Tests/Nequ_Kin4M.faa +0 -2970
  203. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata +0 -0
  204. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt +0 -7
  205. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv +0 -17
  206. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv +0 -137
  207. data/utils/enveomics/Tests/a_mg.cds-go.blast.tsv +0 -123
  208. data/utils/enveomics/Tests/a_mg.reads-cds.blast.tsv +0 -200
  209. data/utils/enveomics/Tests/a_mg.reads-cds.counts.tsv +0 -55
  210. data/utils/enveomics/Tests/alkB.nwk +0 -1
  211. data/utils/enveomics/Tests/anthrax-cansnp-data.tsv +0 -13
  212. data/utils/enveomics/Tests/anthrax-cansnp-key.tsv +0 -17
  213. data/utils/enveomics/Tests/hiv1.faa +0 -59
  214. data/utils/enveomics/Tests/hiv1.fna +0 -134
  215. data/utils/enveomics/Tests/hiv2.faa +0 -70
  216. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv +0 -233
  217. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim +0 -1
  218. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec +0 -233
  219. data/utils/enveomics/Tests/phyla_counts.tsv +0 -10
  220. data/utils/enveomics/Tests/primate_lentivirus.ogs +0 -11
  221. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm +0 -9
  222. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm +0 -8
  223. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm +0 -6
  224. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm +0 -9
  225. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm +0 -6
  226. data/utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm +0 -6
  227. data/utils/enveomics/build_enveomics_r.bash +0 -45
  228. data/utils/enveomics/enveomics.R/DESCRIPTION +0 -31
  229. data/utils/enveomics/enveomics.R/NAMESPACE +0 -39
  230. data/utils/enveomics/enveomics.R/R/autoprune.R +0 -155
  231. data/utils/enveomics/enveomics.R/R/barplot.R +0 -184
  232. data/utils/enveomics/enveomics.R/R/cliopts.R +0 -135
  233. data/utils/enveomics/enveomics.R/R/df2dist.R +0 -154
  234. data/utils/enveomics/enveomics.R/R/growthcurve.R +0 -331
  235. data/utils/enveomics/enveomics.R/R/prefscore.R +0 -79
  236. data/utils/enveomics/enveomics.R/R/recplot.R +0 -354
  237. data/utils/enveomics/enveomics.R/R/recplot2.R +0 -1631
  238. data/utils/enveomics/enveomics.R/R/tribs.R +0 -583
  239. data/utils/enveomics/enveomics.R/R/utils.R +0 -80
  240. data/utils/enveomics/enveomics.R/README.md +0 -81
  241. data/utils/enveomics/enveomics.R/data/growth.curves.rda +0 -0
  242. data/utils/enveomics/enveomics.R/data/phyla.counts.rda +0 -0
  243. data/utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd +0 -16
  244. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd +0 -16
  245. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd +0 -16
  246. data/utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd +0 -25
  247. data/utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd +0 -46
  248. data/utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd +0 -23
  249. data/utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd +0 -47
  250. data/utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd +0 -23
  251. data/utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd +0 -23
  252. data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd +0 -40
  253. data/utils/enveomics/enveomics.R/man/enve.barplot.Rd +0 -103
  254. data/utils/enveomics/enveomics.R/man/enve.cliopts.Rd +0 -67
  255. data/utils/enveomics/enveomics.R/man/enve.col.alpha.Rd +0 -24
  256. data/utils/enveomics/enveomics.R/man/enve.col2alpha.Rd +0 -19
  257. data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd +0 -45
  258. data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd +0 -44
  259. data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd +0 -47
  260. data/utils/enveomics/enveomics.R/man/enve.growthcurve.Rd +0 -75
  261. data/utils/enveomics/enveomics.R/man/enve.prefscore.Rd +0 -50
  262. data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd +0 -44
  263. data/utils/enveomics/enveomics.R/man/enve.recplot.Rd +0 -139
  264. data/utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd +0 -45
  265. data/utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd +0 -24
  266. data/utils/enveomics/enveomics.R/man/enve.recplot2.Rd +0 -77
  267. data/utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd +0 -25
  268. data/utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd +0 -21
  269. data/utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd +0 -19
  270. data/utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd +0 -19
  271. data/utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd +0 -47
  272. data/utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd +0 -29
  273. data/utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd +0 -18
  274. data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd +0 -45
  275. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd +0 -36
  276. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd +0 -19
  277. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd +0 -19
  278. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd +0 -27
  279. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd +0 -52
  280. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd +0 -17
  281. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd +0 -51
  282. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd +0 -43
  283. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd +0 -82
  284. data/utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd +0 -59
  285. data/utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd +0 -27
  286. data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd +0 -36
  287. data/utils/enveomics/enveomics.R/man/enve.selvector.Rd +0 -23
  288. data/utils/enveomics/enveomics.R/man/enve.tribs.Rd +0 -68
  289. data/utils/enveomics/enveomics.R/man/enve.tribs.test.Rd +0 -28
  290. data/utils/enveomics/enveomics.R/man/enve.truncate.Rd +0 -27
  291. data/utils/enveomics/enveomics.R/man/growth.curves.Rd +0 -14
  292. data/utils/enveomics/enveomics.R/man/phyla.counts.Rd +0 -13
  293. data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd +0 -78
  294. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd +0 -46
  295. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd +0 -45
  296. data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd +0 -125
  297. data/utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd +0 -19
  298. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd +0 -19
  299. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd +0 -19
  300. data/utils/enveomics/globals.mk +0 -8
  301. data/utils/enveomics/manifest.json +0 -9
  302. data/utils/multitrim/Multitrim How-To.pdf +0 -0
  303. data/utils/multitrim/README.md +0 -67
  304. data/utils/multitrim/multitrim.py +0 -1555
  305. data/utils/multitrim/multitrim.yml +0 -13
data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt DELETED
@@ -1,7 +0,0 @@
1
- GCF_001042745.1_ASM104274v1_protein
2
- GCF_001042775.1_ASM104277v1_protein
3
- GCF_001042795.1_ASM104279v1_protein
4
- GCF_001042855.1_ASM104285v1_protein
5
- GCF_001042875.1_ASM104287v1_protein
6
- GCF_001466505.1_ASM146650v1_protein
7
- GCF_001021915.1_ASM102191v1_protein
data/utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv DELETED
@@ -1,17 +0,0 @@
1
- GCF_000007385.1_ASM738v1_protein GCF_000010025.1_ASM1002v1_protein GCF_000019585.2_ASM1958v2_protein GCF_000168315.3_ASM16831v3_protein GCF_000940825.1_ASM94082v1_protein GCF_000948075.1_ASM94807v1_protein GCF_001021915.1_ASM102191v1_protein GCF_001042735.1_ASM104273v1_protein GCF_001042745.1_ASM104274v1_protein GCF_001042775.1_ASM104277v1_protein GCF_001042795.1_ASM104279v1_protein GCF_001042815.1_ASM104281v1_protein GCF_001042835.1_ASM104283v1_protein GCF_001042855.1_ASM104285v1_protein GCF_001042875.1_ASM104287v1_protein GCF_001466505.1_ASM146650v1_protein
2
- GCF_000007385.1_ASM738v1_protein 0 0.00280999449339106 0.004857341269839 0.027082634730539 0.02900279237845 0.004199687233438 0.029323490378236 0.027393856209151 0.027273575638506 0.026308349705304 0.026557204658903 0.0292356005308559 0.029200662471017 0.027184534731323 0.0272492292554929 0.027051188051595
3
- GCF_000010025.1_ASM1002v1_protein 0.00280999449339106 0 0.00547010022271607 0.0262509458577949 0.02797165430506 0.00365342849146501 0.0273582377988851 0.0258542857142849 0.0260377212745399 0.025122290125442 0.0247799738219879 0.0274411514556731 0.028243164763457 0.0259861835748779 0.026161521108603 0.0267200800533681
4
- GCF_000019585.2_ASM1958v2_protein 0.004857341269839 0.00547010022271607 0 0.0258787254901971 0.028623235578473 0.00365574268359893 0.02646489396411 0.0262814707771371 0.025405944730078 0.026916317991633 0.02515978367748 0.028336449511402 0.028484099055069 0.025353365539453 0.0253547649710239 0.026663594009983
5
- GCF_000168315.3_ASM16831v3_protein 0.027082634730539 0.0262509458577949 0.0258787254901971 0 0.00867199519230994 0.0265598635034139 0.00614387096774294 0.000627776254456052 0.00318137791871095 0.00289319884726396 0.00575849507315695 0.00821546762590103 0.00809347500748501 0.00329896253602499 0.00312418281747398 0.025921796565391
6
- GCF_000940825.1_ASM94082v1_protein 0.02900279237845 0.02797165430506 0.028623235578473 0.00867199519230994 0 0.027987924281985 0.010140723844282 0.00999447870778397 0.010986664677804 0.010223044776118 0.00676966426858399 0.004718089430893 0.00497302784222597 0.010946851686063 0.010912578616351 0.025502212681638
7
- GCF_000948075.1_ASM94807v1_protein 0.004199687233438 0.00365342849146501 0.00365574268359893 0.0265598635034139 0.027987924281985 0 0.027760875331565 0.028046350129199 0.026720078099578 0.026611856677526 0.025358619561662 0.026601176470589 0.0270234833659499 0.026558800521514 0.026872946544982 0.0269170163170141
8
- GCF_001021915.1_ASM102191v1_protein 0.029323490378236 0.0273582377988851 0.02646489396411 0.00614387096774294 0.010140723844282 0.027760875331565 0 0.00636614645858501 0.005477464361541 0.00704475121359195 0.00198806732792306 0.009384763948498 0.00909632578077193 0.00570916818457803 0.00547627737226307 0.0258182184873949
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- GCF_001042795.1_ASM104279v1_protein 0.026557204658903 0.0247799738219879 0.02515978367748 0.00575849507315695 0.00676966426858399 0.025358619561662 0.00198806732792306 0.00623691115086601 0.00531255242660293 0.00536479928100704 0 0.00573288409703494 0.005716656698565 0.00519721640227601 0.00524243609022705 0.0249705158069909
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- GCF_001042855.1_ASM104285v1_protein 0.027184534731323 0.0259861835748779 0.025353365539453 0.00329896253602499 0.010946851686063 0.026558800521514 0.00570916818457803 0.00348153538812994 0.000916337719299065 0.00191674495716995 0.00519721640227601 0.00926569960713195 0.00887172143503193 0 0.000910245111540036 0.025238844621516
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data/utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv DELETED
@@ -1,137 +0,0 @@
1
- SeqA SeqB AAI SD N Omega Frx
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data/utils/enveomics/Tests/a_mg.cds-go.blast.tsv DELETED
@@ -1,123 +0,0 @@
1
- A:8 GO:0003677 25.27 281 180 11 106 369 33 300 9e-14 77.4 438 1074
2
- A:8 GO:0004386 25.27 281 180 11 106 369 33 300 9e-14 77.4 438 1074
3
- A:8 GO:0004520 25.27 281 180 11 106 369 33 300 9e-14 77.4 438 1074
4
- A:8 GO:0005524 25.27 281 180 11 106 369 33 300 9e-14 77.4 438 1074
5
- A:8 GO:0006281 25.27 281 180 11 106 369 33 300 9e-14 77.4 438 1074
6
- A:8 GO:0008270 25.27 281 180 11 106 369 33 300 9e-14 77.4 438 1074
7
- A:8 GO:0009411 25.27 281 180 11 106 369 33 300 9e-14 77.4 438 1074
8
- A:8 GO:0031297 25.27 281 180 11 106 369 33 300 9e-14 77.4 438 1074
9
- A:8 GO:0036292 25.27 281 180 11 106 369 33 300 9e-14 77.4 438 1074
10
- A:8 GO:0036310 25.27 281 180 11 106 369 33 300 9e-14 77.4 438 1074
11
- A:8 GO:0043596 25.27 281 180 11 106 369 33 300 9e-14 77.4 438 1074
12
- A:8 GO:0045910 25.27 281 180 11 106 369 33 300 9e-14 77.4 438 1074
13
- A:8 GO:0048478 25.27 281 180 11 106 369 33 300 9e-14 77.4 438 1074
14
- A:8 GO:0070530 25.27 281 180 11 106 369 33 300 9e-14 77.4 438 1074
15
- A:28 GO:0004748 33.97 527 289 14 81 574 192 692 8e-77 263 584 692
16
- A:28 GO:0005524 33.97 527 289 14 81 574 192 692 8e-77 263 584 692
17
- A:28 GO:0005618 33.97 527 289 14 81 574 192 692 8e-77 263 584 692
18
- A:28 GO:0005829 33.97 527 289 14 81 574 192 692 8e-77 263 584 692
19
- A:28 GO:0005886 33.97 527 289 14 81 574 192 692 8e-77 263 584 692
20
- A:28 GO:0005971 33.97 527 289 14 81 574 192 692 8e-77 263 584 692
21
- A:28 GO:0006260 33.97 527 289 14 81 574 192 692 8e-77 263 584 692
22
- A:28 GO:0031419 33.97 527 289 14 81 574 192 692 8e-77 263 584 692
23
- A:30 GO:0005737 31.32 431 284 7 72 500 3 423 5e-68 230 504 426
24
- A:30 GO:0007049 31.32 431 284 7 72 500 3 423 5e-68 230 504 426
25
- A:30 GO:0008360 31.32 431 284 7 72 500 3 423 5e-68 230 504 426
26
- A:30 GO:0008760 31.32 431 284 7 72 500 3 423 5e-68 230 504 426
27
- A:30 GO:0009252 31.32 431 284 7 72 500 3 423 5e-68 230 504 426
28
- A:30 GO:0019277 31.32 431 284 7 72 500 3 423 5e-68 230 504 426
29
- A:30 GO:0051301 31.32 431 284 7 72 500 3 423 5e-68 230 504 426
30
- A:31 GO:0003677 28.03 446 295 11 128 558 233 667 3e-36 148 631 753
31
- A:31 GO:0005524 28.03 446 295 11 128 558 233 667 3e-36 148 631 753
32
- A:31 GO:0006269 28.03 446 295 11 128 558 233 667 3e-36 148 631 753
33
- A:31 GO:0008026 28.03 446 295 11 128 558 233 667 3e-36 148 631 753
34
- A:31 GO:0046872 28.03 446 295 11 128 558 233 667 3e-36 148 631 753
35
- A:31 GO:1990077 28.03 446 295 11 128 558 233 667 3e-36 148 631 753
36
- A:32 GO:0005506 38.46 169 96 5 8 176 9 169 1e-28 110 176 181
37
- A:32 GO:0006412 38.46 169 96 5 8 176 9 169 1e-28 110 176 181
38
- A:32 GO:0042586 38.46 169 96 5 8 176 9 169 1e-28 110 176 181
39
- A:33 GO:0004479 40.47 299 151 6 5 279 2 297 6e-58 194 282 309
40
- A:33 GO:0006413 40.47 299 151 6 5 279 2 297 6e-58 194 282 309
41
- A:39 GO:0004008 43.26 638 350 8 9 639 58 690 4e-176 524 643 690
42
- A:39 GO:0005524 43.26 638 350 8 9 639 58 690 4e-176 524 643 690
43
- A:39 GO:0005886 43.26 638 350 8 9 639 58 690 4e-176 524 643 690
44
- A:39 GO:0016021 43.26 638 350 8 9 639 58 690 4e-176 524 643 690
45
- A:39 GO:0046872 43.26 638 350 8 9 639 58 690 4e-176 524 643 690
46
- A:39 GO:0060003 43.26 638 350 8 9 639 58 690 4e-176 524 643 690
47
- A:42 GO:0003677 44.58 83 46 0 6 88 18 100 4e-18 77.4 89 101
48
- A:42 GO:0005737 44.58 83 46 0 6 88 18 100 4e-18 77.4 89 101
49
- A:42 GO:0006351 44.58 83 46 0 6 88 18 100 4e-18 77.4 89 101
50
- A:42 GO:0006355 44.58 83 46 0 6 88 18 100 4e-18 77.4 89 101
51
- A:42 GO:0046872 44.58 83 46 0 6 88 18 100 4e-18 77.4 89 101
52
- A:45 GO:0005886 40.59 239 136 3 26 263 20 253 6e-54 181 264 264
53
- A:45 GO:0016021 40.59 239 136 3 26 263 20 253 6e-54 181 264 264
54
- A:48 GO:0004497 27.83 327 221 8 8 330 4 319 7e-19 91.7 404 499
55
- A:48 GO:0019439 27.83 327 221 8 8 330 4 319 7e-19 91.7 404 499
56
- A:54 GO:0003677 36.84 133 74 5 13 138 10 139 2e-16 75.9 141 144
57
- A:54 GO:0003700 36.84 133 74 5 13 138 10 139 2e-16 75.9 141 144
58
- A:54 GO:0005737 36.84 133 74 5 13 138 10 139 2e-16 75.9 141 144
59
- A:54 GO:0006351 36.84 133 74 5 13 138 10 139 2e-16 75.9 141 144
60
- A:54 GO:0046872 36.84 133 74 5 13 138 10 139 2e-16 75.9 141 144
61
- A:55 GO:0003677 43.75 64 35 1 1 63 1 64 2e-12 61.2 66 67
62
- A:55 GO:0005737 43.75 64 35 1 1 63 1 64 2e-12 61.2 66 67
63
- A:55 GO:0006351 43.75 64 35 1 1 63 1 64 2e-12 61.2 66 67
64
- A:55 GO:0006355 43.75 64 35 1 1 63 1 64 2e-12 61.2 66 67
65
- A:55 GO:0006950 43.75 64 35 1 1 63 1 64 2e-12 61.2 66 67
66
- A:56 GO:0003924 50.84 598 286 4 3 594 4 599 0.0 624 596 599
67
- A:56 GO:0005525 50.84 598 286 4 3 594 4 599 0.0 624 596 599
68
- A:56 GO:0006184 50.84 598 286 4 3 594 4 599 0.0 624 596 599
69
- A:71 GO:0005886 25.35 288 203 6 61 346 128 405 7e-15 80.5 415 776
70
- A:71 GO:0006810 25.35 288 203 6 61 346 128 405 7e-15 80.5 415 776
71
- A:71 GO:0016021 25.35 288 203 6 61 346 128 405 7e-15 80.5 415 776
72
- A:71 GO:0016787 25.35 288 203 6 61 346 128 405 7e-15 80.5 415 776
73
- A:71 GO:0030420 25.35 288 203 6 61 346 128 405 7e-15 80.5 415 776
74
- A:72 GO:0004523 47.15 123 60 3 9 129 8 127 8e-24 98.2 135 364
75
- A:72 GO:0006401 47.15 123 60 3 9 129 8 127 8e-24 98.2 135 364
76
- A:72 GO:0009236 47.15 123 60 3 9 129 8 127 8e-24 98.2 135 364
77
- A:72 GO:0032296 47.15 123 60 3 9 129 8 127 8e-24 98.2 135 364
78
- A:72 GO:0043755 47.15 123 60 3 9 129 8 127 8e-24 98.2 135 364
79
- A:72 GO:0071667 47.15 123 60 3 9 129 8 127 8e-24 98.2 135 364
80
- A:74 GO:0003677 32.62 561 333 11 27 573 30 559 3e-85 287 575 786
81
- A:74 GO:0006281 32.62 561 333 11 27 573 30 559 3e-85 287 575 786
82
- A:74 GO:0006310 32.62 561 333 11 27 573 30 559 3e-85 287 575 786
83
- A:74 GO:0008409 32.62 561 333 11 27 573 30 559 3e-85 287 575 786
84
- A:74 GO:0030145 32.62 561 333 11 27 573 30 559 3e-85 287 575 786
85
- A:74 GO:0090305 32.62 561 333 11 27 573 30 559 3e-85 287 575 786
86
- A:76 GO:0004618 41.09 387 205 7 9 372 10 396 2e-82 263 372 396
87
- A:76 GO:0005524 41.09 387 205 7 9 372 10 396 2e-82 263 372 396
88
- A:76 GO:0005737 41.09 387 205 7 9 372 10 396 2e-82 263 372 396
89
- A:76 GO:0006096 41.09 387 205 7 9 372 10 396 2e-82 263 372 396
90
- A:77 GO:0004807 36.51 252 148 5 2 247 4 249 9e-47 162 248 252
91
- A:77 GO:0005737 36.51 252 148 5 2 247 4 249 9e-47 162 248 252
92
- A:77 GO:0006094 36.51 252 148 5 2 247 4 249 9e-47 162 248 252
93
- A:77 GO:0006096 36.51 252 148 5 2 247 4 249 9e-47 162 248 252
94
- A:77 GO:0006098 36.51 252 148 5 2 247 4 249 9e-47 162 248 252
95
- A:81 GO:0005886 29.10 402 278 4 3 400 4 402 6e-57 197 402 406
96
- A:81 GO:0008565 29.10 402 278 4 3 400 4 402 6e-57 197 402 406
97
- A:81 GO:0009306 29.10 402 278 4 3 400 4 402 6e-57 197 402 406
98
- A:81 GO:0015627 29.10 402 278 4 3 400 4 402 6e-57 197 402 406
99
- A:81 GO:0015628 29.10 402 278 4 3 400 4 402 6e-57 197 402 406
100
- A:81 GO:0016021 29.10 402 278 4 3 400 4 402 6e-57 197 402 406
101
- A:82 GO:0005524 39.45 583 310 8 9 581 17 566 2e-120 374 581 567
102
- A:82 GO:0005737 39.45 583 310 8 9 581 17 566 2e-120 374 581 567
103
- A:82 GO:0008565 39.45 583 310 8 9 581 17 566 2e-120 374 581 567
104
- A:82 GO:0015627 39.45 583 310 8 9 581 17 566 2e-120 374 581 567
105
- A:82 GO:0015628 39.45 583 310 8 9 581 17 566 2e-120 374 581 567
106
- A:82 GO:0017111 39.45 583 310 8 9 581 17 566 2e-120 374 581 567
107
- A:83 GO:0003700 45.14 350 173 3 13 362 9 339 1e-93 292 398 382
108
- A:83 GO:0003723 45.14 350 173 3 13 362 9 339 1e-93 292 398 382
109
- A:83 GO:0005737 45.14 350 173 3 13 362 9 339 1e-93 292 398 382
110
- A:83 GO:0006353 45.14 350 173 3 13 362 9 339 1e-93 292 398 382
111
- A:83 GO:0031564 45.14 350 173 3 13 362 9 339 1e-93 292 398 382
112
- A:91 GO:0003697 29.57 487 298 14 2 464 75 540 4e-49 182 482 566
113
- A:91 GO:0003896 29.57 487 298 14 2 464 75 540 4e-49 182 482 566
114
- A:91 GO:0005524 29.57 487 298 14 2 464 75 540 4e-49 182 482 566
115
- A:91 GO:0008270 29.57 487 298 14 2 464 75 540 4e-49 182 482 566
116
- A:91 GO:0032508 29.57 487 298 14 2 464 75 540 4e-49 182 482 566
117
- A:91 GO:0043139 29.57 487 298 14 2 464 75 540 4e-49 182 482 566
118
- A:91 GO:1990077 29.57 487 298 14 2 464 75 540 4e-49 182 482 566
119
- A:94 GO:0003677 37.13 544 251 14 1 459 167 704 2e-94 306 459 704
120
- A:94 GO:0003887 37.13 544 251 14 1 459 167 704 2e-94 306 459 704
121
- A:94 GO:0004527 37.13 544 251 14 1 459 167 704 2e-94 306 459 704
122
- A:94 GO:0019048 37.13 544 251 14 1 459 167 704 2e-94 306 459 704
123
- A:94 GO:0090305 37.13 544 251 14 1 459 167 704 2e-94 306 459 704
data/utils/enveomics/Tests/a_mg.reads-cds.blast.tsv DELETED
@@ -1,200 +0,0 @@
1
- HISEQ:151:C0KDYACXX:7:1101:9010:33594_2:N:0:ATCACG A:91 100.00 101 0 0 1 101 291 191 3.4e-51 199.0 101
2
- HISEQ:151:C0KDYACXX:7:1102:19611:107640_2:N:0:ATCACG A:94 100.00 101 0 0 1 101 1358 1258 3.0e-51 199.0 101
3
- HISEQ:151:C0KDYACXX:7:1103:15070:177978_2:N:0:ATCACG A:94 100.00 101 0 0 1 101 164 64 2.3e-51 200.0 101
4
- HISEQ:151:C0KDYACXX:7:1103:8861:144158_2:N:0:ATCACG A:40 100.00 101 0 0 1 101 116 16 1.6e-50 197.0 101
5
- HISEQ:151:C0KDYACXX:7:1104:13044:83532_2:N:0:ATCACG A:19 100.00 101 0 0 1 101 467 367 2.7e-50 196.0 101
6
- HISEQ:151:C0KDYACXX:7:1104:17642:118598_2:N:0:ATCACG A:43 100.00 101 0 0 1 101 165 65 3.9e-51 199.0 101
7
- HISEQ:151:C0KDYACXX:7:1104:4272:131221_2:N:0:ATCACG A:77 100.00 101 0 0 1 101 406 506 6.5e-51 198.0 101
8
- HISEQ:151:C0KDYACXX:7:1105:18472:118873_2:N:0:ATCACG A:78 100.00 101 0 0 1 101 1252 1352 1.8e-50 197.0 101
9
- HISEQ:151:C0KDYACXX:7:1105:8403:24966_2:N:0:ATCACG A:81 100.00 101 0 0 1 101 733 833 6.5e-51 198.0 101
10
- HISEQ:151:C0KDYACXX:7:1107:4952:167394_2:N:0:ATCACG A:79 100.00 101 0 0 1 101 203 103 2.3e-51 200.0 101
11
- HISEQ:151:C0KDYACXX:7:1108:18968:102814_2:N:0:ATCACG A:19 100.00 54 0 0 1 54 1782 1835 1.4e-22 104.0 54
12
- HISEQ:151:C0KDYACXX:7:1203:17588:135814_2:N:0:ATCACG A:94 100.00 101 0 0 1 101 1242 1142 1.6e-50 197.0 101
13
- HISEQ:151:C0KDYACXX:7:1203:5393:135404_2:N:0:ATCACG A:71 100.00 101 0 0 1 101 871 771 1.8e-50 197.0 101
14
- HISEQ:151:C0KDYACXX:7:1204:15877:16474_2:N:0:ATCACG A:64 100.00 101 0 0 1 101 1814 1714 3.4e-51 199.0 101
15
- HISEQ:151:C0KDYACXX:7:1206:11936:42934_2:N:0:ATCACG A:7 100.00 101 0 0 1 101 116 216 1.6e-50 197.0 101
16
- HISEQ:151:C0KDYACXX:7:1206:17264:122150_2:N:0:ATCACG A:82 100.00 101 0 0 1 101 143 243 8.4e-51 198.0 101
17
- HISEQ:151:C0KDYACXX:7:1206:7270:126143_2:N:0:ATCACG A:37 100.00 101 0 0 1 101 317 417 4.4e-51 199.0 101
18
- HISEQ:151:C0KDYACXX:7:1208:13735:19904_2:N:0:ATCACG A:19 100.00 101 0 0 1 101 2215 2315 3.9e-50 196.0 101
19
- HISEQ:151:C0KDYACXX:7:1208:15154:182301_2:N:0:ATCACG A:32 100.00 98 0 0 1 98 147 244 6.8e-49 191.0 98
20
- HISEQ:151:C0KDYACXX:7:1303:2144:114940_2:N:0:ATCACG A:8 100.00 99 0 0 3 101 854 756 1.1e-49 194.0 101
21
- HISEQ:151:C0KDYACXX:7:1304:17476:183294_2:N:0:ATCACG A:47 100.00 101 0 0 1 101 798 698 5.1e-50 195.0 101
22
- HISEQ:151:C0KDYACXX:7:1304:3738:73278_2:N:0:ATCACG A:77 100.00 101 0 0 1 101 330 230 4.4e-51 199.0 101
23
- HISEQ:151:C0KDYACXX:7:1306:13389:25254_2:N:0:ATCACG A:56 100.00 101 0 0 1 101 1681 1781 1.2e-50 197.0 101
24
- HISEQ:151:C0KDYACXX:7:1306:6571:15911_2:N:0:ATCACG A:56 100.00 70 0 0 1 70 969 1038 1.9e-32 137.0 70
25
- HISEQ:151:C0KDYACXX:7:1306:6992:156479_2:N:0:ATCACG A:94 100.00 101 0 0 1 101 238 338 2.7e-51 199.0 101
26
- HISEQ:151:C0KDYACXX:7:1307:6357:48224_2:N:0:ATCACG A:35 100.00 100 0 0 1 100 100 1 1.6e-49 194.0 101
27
- HISEQ:151:C0KDYACXX:7:2102:1854:11252_2:N:0:ATCACG A:84 99.01 101 1 0 1 101 1723 1823 1.9e-50 197.0 101
28
- HISEQ:151:C0KDYACXX:7:2105:17491:151636_2:N:0:ATCACG A:43 100.00 101 0 0 1 101 376 476 2.1e-50 197.0 101
29
- HISEQ:151:C0KDYACXX:7:2106:14976:11490_2:N:0:ATCACG A:65 100.00 101 0 0 1 101 872 772 6.5e-51 198.0 101
30
- HISEQ:151:C0KDYACXX:7:2106:2511:169844_2:N:0:ATCACG A:74 100.00 70 0 0 1 70 366 435 1.9e-32 137.0 70
31
- HISEQ:151:C0KDYACXX:7:2107:15386:119865_2:N:0:ATCACG A:91 100.00 70 0 0 1 70 152 221 8.8e-33 138.0 70
32
- HISEQ:151:C0KDYACXX:7:2108:15621:20519_2:N:0:ATCACG A:43 100.00 55 0 0 1 55 134 80 8.4e-24 108.0 55
33
- HISEQ:151:C0KDYACXX:7:2204:19754:154528_2:N:0:ATCACG A:79 100.00 101 0 0 1 101 321 221 1.8e-50 197.0 101
34
- HISEQ:151:C0KDYACXX:7:2205:9237:74825_2:N:0:ATCACG A:73 100.00 70 0 0 1 70 887 818 8.8e-33 138.0 70
35
- HISEQ:151:C0KDYACXX:7:2207:1873:68479_2:N:0:ATCACG A:43 100.00 101 0 0 1 101 215 315 1.4e-50 197.0 101
36
- HISEQ:151:C0KDYACXX:7:2208:2545:16021_2:N:0:ATCACG A:28 100.00 101 0 0 1 101 71 171 3.0e-50 196.0 101
37
- HISEQ:151:C0KDYACXX:7:2303:10238:86402_2:N:0:ATCACG A:47 100.00 101 0 0 1 101 223 323 1.6e-50 197.0 101
38
- HISEQ:151:C0KDYACXX:7:2303:13321:108856_2:N:0:ATCACG A:56 100.00 101 0 0 1 101 432 532 5.7e-51 198.0 101
39
- HISEQ:151:C0KDYACXX:7:2303:14401:16637_2:N:0:ATCACG A:7 100.00 101 0 0 1 101 194 94 1.8e-50 197.0 101
40
- HISEQ:151:C0KDYACXX:7:2304:14385:126743_2:N:0:ATCACG A:81 100.00 101 0 0 1 101 156 256 9.6e-51 198.0 101
41
- HISEQ:151:C0KDYACXX:7:2304:16857:102620_2:N:0:ATCACG A:18 100.00 96 0 0 6 101 99 4 7.0e-47 185.0 101
42
- HISEQ:151:C0KDYACXX:7:2305:7853:149467_2:N:0:ATCACG A:81 100.00 101 0 0 1 101 205 105 3.9e-50 196.0 101
43
- HISEQ:151:C0KDYACXX:7:2307:10442:33789_2:N:0:ATCACG A:94 100.00 73 0 0 1 73 1290 1362 2.1e-34 143.0 73
44
- HISEQ:151:C0KDYACXX:7:2307:9791:78234_2:N:0:ATCACG A:19 100.00 87 0 0 1 87 2331 2245 9.0e-42 168.0 87
45
- HISEQ:151:C0KDYACXX:7:2308:10162:164935_2:N:0:ATCACG A:53 100.00 101 0 0 1 101 813 713 7.4e-51 198.0 101
46
- HISEQ:151:C0KDYACXX:7:1101:10060:51121_1:N:0:ATCACG A:73 100.00 101 0 0 1 101 498 598 1.8e-50 197.0 101
47
- HISEQ:151:C0KDYACXX:7:1101:16947:195237_1:N:0:ATCACG A:6 100.00 101 0 0 1 101 933 833 3.4e-50 196.0 101
48
- HISEQ:151:C0KDYACXX:7:1103:19419:150175_1:N:0:ATCACG A:65 100.00 101 0 0 1 101 1379 1279 5.7e-51 198.0 101
49
- HISEQ:151:C0KDYACXX:7:1103:8054:79579_1:N:0:ATCACG A:8 100.00 101 0 0 1 101 194 94 2.1e-50 197.0 101
50
- HISEQ:151:C0KDYACXX:7:1104:2529:85801_1:N:0:ATCACG A:31 100.00 99 0 0 3 101 718 620 1.6e-49 194.0 101
51
- HISEQ:151:C0KDYACXX:7:1105:9594:26952_1:N:0:ATCACG A:8 100.00 92 0 0 1 92 525 616 2.1e-45 180.0 92
52
- HISEQ:151:C0KDYACXX:7:1106:12695:70232_1:N:0:ATCACG A:63 100.00 101 0 0 1 101 135 35 5.7e-51 198.0 101
53
- HISEQ:151:C0KDYACXX:7:1106:19998:57320_1:N:0:ATCACG A:81 100.00 96 0 0 6 101 1209 1114 1.9e-47 187.0 101
54
- HISEQ:151:C0KDYACXX:7:1107:5517:120520_1:N:0:ATCACG A:40 100.00 101 0 0 1 101 307 407 8.4e-51 198.0 101
55
- HISEQ:151:C0KDYACXX:7:1108:3262:193005_1:N:0:ATCACG A:94 100.00 101 0 0 1 101 964 1064 5.7e-51 198.0 101
56
- HISEQ:151:C0KDYACXX:7:1202:10888:6977_1:N:0:ATCACG A:84 99.01 101 1 0 1 101 1736 1636 2.2e-50 196.0 101
57
- HISEQ:151:C0KDYACXX:7:1203:13940:15109_1:N:0:ATCACG A:76 100.00 101 0 0 1 101 181 281 7.4e-51 198.0 101
58
- HISEQ:151:C0KDYACXX:7:1203:3444:172558_1:N:0:ATCACG A:84 100.00 91 0 0 1 91 648 738 3.5e-45 179.0 91
59
- HISEQ:151:C0KDYACXX:7:1206:14315:130502_1:N:0:ATCACG A:64 100.00 101 0 0 1 101 779 679 8.4e-51 198.0 101
60
- HISEQ:151:C0KDYACXX:7:1206:14322:19426_1:N:0:ATCACG A:35 100.00 101 0 0 1 101 181 81 5.1e-51 199.0 101
61
- HISEQ:151:C0KDYACXX:7:1206:9836:167775_1:N:0:ATCACG A:65 100.00 87 0 0 1 87 631 717 2.5e-42 170.0 87
62
- HISEQ:151:C0KDYACXX:7:1207:9463:54302_1:N:0:ATCACG A:53 100.00 100 0 0 1 100 200 299 1.6e-49 194.0 100
63
- HISEQ:151:C0KDYACXX:7:1208:18463:140863_1:N:0:ATCACG A:28 100.00 100 0 0 1 100 307 406 2.1e-50 197.0 100
64
- HISEQ:151:C0KDYACXX:7:1303:9362:35522_1:N:0:ATCACG A:56 100.00 101 0 0 1 101 1592 1492 3.0e-50 196.0 101
65
- HISEQ:151:C0KDYACXX:7:1304:20405:26604_1:N:0:ATCACG A:83 100.00 101 0 0 1 101 595 495 3.0e-51 199.0 101
66
- HISEQ:151:C0KDYACXX:7:1306:14726:97496_1:N:0:ATCACG A:48 100.00 101 0 0 1 101 721 821 1.1e-50 197.0 101
67
- HISEQ:151:C0KDYACXX:7:1306:4457:92158_1:N:0:ATCACG A:64 100.00 89 0 0 1 89 171 83 1.9e-43 173.0 89
68
- HISEQ:151:C0KDYACXX:7:1308:16401:63535_1:N:0:ATCACG A:82 100.00 101 0 0 1 101 26 126 1.2e-50 197.0 101
69
- HISEQ:151:C0KDYACXX:7:2101:12173:68150_1:N:0:ATCACG A:41 100.00 101 0 0 1 101 210 110 2.1e-50 197.0 101
70
- HISEQ:151:C0KDYACXX:7:2102:10997:41422_1:N:0:ATCACG A:81 100.00 101 0 0 1 101 274 174 9.6e-51 198.0 101
71
- HISEQ:151:C0KDYACXX:7:2102:16034:180520_1:N:0:ATCACG A:74 100.00 101 0 0 1 101 224 324 1.1e-50 197.0 101
72
- HISEQ:151:C0KDYACXX:7:2103:4131:43048_1:N:0:ATCACG A:14 99.01 101 1 0 1 101 296 396 1.2e-49 194.0 101
73
- HISEQ:151:C0KDYACXX:7:2104:16103:188297_1:N:0:ATCACG A:73 100.00 92 0 0 1 92 616 525 1.1e-45 181.0 92
74
- HISEQ:151:C0KDYACXX:7:2107:14919:2549_1:N:0:ATCACG A:49 100.00 101 0 0 1 101 106 6 3.0e-51 199.0 101
75
- HISEQ:151:C0KDYACXX:7:2201:17229:87958_1:N:0:ATCACG A:48 100.00 101 0 0 1 101 272 372 1.4e-50 197.0 101
76
- HISEQ:151:C0KDYACXX:7:2201:6461:28885_1:N:0:ATCACG A:94 100.00 99 0 0 1 99 419 517 3.5e-50 196.0 99
77
- HISEQ:151:C0KDYACXX:7:2204:1854:46040_1:N:0:ATCACG A:39 99.01 101 1 0 1 101 497 397 1.3e-49 194.0 101
78
- HISEQ:151:C0KDYACXX:7:2205:11217:131452_1:N:0:ATCACG A:9 100.00 101 0 0 1 101 129 229 2.7e-50 196.0 101
79
- HISEQ:151:C0KDYACXX:7:2205:14128:144458_1:N:0:ATCACG A:78 100.00 100 0 0 1 100 1266 1365 4.5e-50 195.0 100
80
- HISEQ:151:C0KDYACXX:7:2205:2254:8730_1:N:0:ATCACG A:78 100.00 101 0 0 1 101 284 384 1.4e-50 197.0 101
81
- HISEQ:151:C0KDYACXX:7:2206:18099:79528_1:N:0:ATCACG A:28 100.00 72 0 0 1 72 1236 1307 2.1e-33 140.0 72
82
- HISEQ:151:C0KDYACXX:7:2206:20254:51010_1:N:0:ATCACG A:97 100.00 101 0 0 1 101 48 148 2.3e-50 196.0 101
83
- HISEQ:151:C0KDYACXX:7:2207:8535:15953_1:N:0:ATCACG A:64 100.00 83 0 0 1 83 1600 1682 2.6e-40 163.0 83
84
- HISEQ:151:C0KDYACXX:7:2302:17823:68484_1:N:0:ATCACG A:43 100.00 101 0 0 1 101 125 25 5.1e-51 199.0 101
85
- HISEQ:151:C0KDYACXX:7:2302:3190:158657_1:N:0:ATCACG A:37 100.00 101 0 0 1 101 299 199 8.4e-51 198.0 101
86
- HISEQ:151:C0KDYACXX:7:2304:19722:197713_1:N:0:ATCACG A:63 100.00 101 0 0 1 101 2676 2776 2.3e-51 200.0 101
87
- HISEQ:151:C0KDYACXX:7:2304:6194:54369_1:N:0:ATCACG A:76 100.00 87 0 0 1 87 277 191 1.5e-42 170.0 87
88
- HISEQ:151:C0KDYACXX:7:2306:5520:91514_1:N:0:ATCACG A:39 100.00 101 0 0 1 101 126 26 1.1e-50 197.0 101
89
- HISEQ:151:C0KDYACXX:7:2308:16927:169908_1:N:0:ATCACG A:78 98.94 94 1 0 1 94 1255 1348 4.8e-45 179.0 94
90
- HISEQ:151:C0KDYACXX:7:2308:17989:87722_1:N:0:ATCACG A:45 100.00 101 0 0 1 101 697 597 7.4e-51 198.0 101
91
- HISEQ:151:C0KDYACXX:7:2308:6753:44037_1:N:0:ATCACG A:72 100.00 99 0 0 1 99 119 217 1.1e-49 194.0 99
92
- HISEQ:151:C0KDYACXX:7:2308:8435:33639_1:N:0:ATCACG A:63 100.00 101 0 0 1 101 384 484 8.4e-51 198.0 101
93
- HISEQ:151:C0KDYACXX:7:1101:10060:51121_2:N:0:ATCACG A:73 100.00 101 0 0 1 101 478 378 2.1e-50 197.0 101
94
- HISEQ:151:C0KDYACXX:7:1103:19419:150175_2:N:0:ATCACG A:65 100.00 101 0 0 1 101 1556 1656 3.9e-51 199.0 101
95
- HISEQ:151:C0KDYACXX:7:1103:8054:79579_2:N:0:ATCACG A:8 100.00 101 0 0 1 101 214 314 3.4e-51 199.0 101
96
- HISEQ:151:C0KDYACXX:7:1104:2529:85801_2:N:0:ATCACG A:31 100.00 98 0 0 4 101 620 717 6.0e-49 192.0 101
97
- HISEQ:151:C0KDYACXX:7:1105:9594:26952_2:N:0:ATCACG A:8 100.00 54 0 0 1 54 329 276 2.1e-23 107.0 54
98
- HISEQ:151:C0KDYACXX:7:1106:12695:70232_2:N:0:ATCACG A:63 100.00 101 0 0 1 101 190 290 3.9e-51 199.0 101
99
- HISEQ:151:C0KDYACXX:7:1106:17840:106174_2:N:0:ATCACG A:57 100.00 99 0 0 3 101 360 262 3.1e-49 193.0 101
100
- HISEQ:151:C0KDYACXX:7:1106:3155:27881_2:N:0:ATCACG A:72 100.00 101 0 0 1 101 371 271 2.7e-50 196.0 101
101
- HISEQ:151:C0KDYACXX:7:1107:5517:120520_2:N:0:ATCACG A:40 100.00 101 0 0 1 101 306 206 1.1e-50 197.0 101
102
- HISEQ:151:C0KDYACXX:7:1108:3262:193005_2:N:0:ATCACG A:94 100.00 101 0 0 1 101 972 872 3.9e-51 199.0 101
103
- HISEQ:151:C0KDYACXX:7:1202:10888:6977_2:N:0:ATCACG A:84 100.00 101 0 0 1 101 1751 1851 2.7e-51 199.0 101
104
- HISEQ:151:C0KDYACXX:7:1203:13940:15109_2:N:0:ATCACG A:76 100.00 101 0 0 1 101 119 19 9.6e-51 198.0 101
105
- HISEQ:151:C0KDYACXX:7:1203:3444:172558_2:N:0:ATCACG A:84 100.00 64 0 0 1 64 508 445 3.0e-29 126.0 64
106
- HISEQ:151:C0KDYACXX:7:1206:14315:130502_2:N:0:ATCACG A:64 100.00 101 0 0 1 101 808 908 8.4e-51 198.0 101
107
- HISEQ:151:C0KDYACXX:7:1206:14322:19426_2:N:0:ATCACG A:35 100.00 101 0 0 1 101 157 257 5.1e-51 199.0 101
108
- HISEQ:151:C0KDYACXX:7:1206:9836:167775_2:N:0:ATCACG A:65 100.00 101 0 0 1 101 587 487 9.6e-51 198.0 101
109
- HISEQ:151:C0KDYACXX:7:1207:9463:54302_2:N:0:ATCACG A:53 100.00 101 0 0 1 101 236 136 2.3e-50 196.0 101
110
- HISEQ:151:C0KDYACXX:7:1208:18463:140863_2:N:0:ATCACG A:28 100.00 101 0 0 1 101 234 134 2.3e-50 196.0 101
111
- HISEQ:151:C0KDYACXX:7:1303:9362:35522_2:N:0:ATCACG A:56 100.00 101 0 0 1 101 1590 1690 2.3e-50 196.0 101
112
- HISEQ:151:C0KDYACXX:7:1304:20405:26604_2:N:0:ATCACG A:83 99.01 101 1 0 1 101 594 694 1.2e-49 194.0 101
113
- HISEQ:151:C0KDYACXX:7:1306:14726:97496_2:N:0:ATCACG A:48 100.00 101 0 0 1 101 666 566 9.6e-51 198.0 101
114
- HISEQ:151:C0KDYACXX:7:1306:2635:186893_2:N:0:ATCACG A:50 100.00 101 0 0 1 101 15 115 1.6e-50 197.0 101
115
- HISEQ:151:C0KDYACXX:7:1306:4457:92158_2:N:0:ATCACG A:64 100.00 101 0 0 1 101 283 383 8.4e-51 198.0 101
116
- HISEQ:151:C0KDYACXX:7:2101:12173:68150_2:N:0:ATCACG A:41 100.00 101 0 0 1 101 180 280 6.5e-51 198.0 101
117
- HISEQ:151:C0KDYACXX:7:2102:10997:41422_2:N:0:ATCACG A:81 100.00 101 0 0 1 101 407 507 1.4e-50 197.0 101
118
- HISEQ:151:C0KDYACXX:7:2102:16034:180520_2:N:0:ATCACG A:74 100.00 87 0 0 1 87 150 64 6.1e-43 172.0 87
119
- HISEQ:151:C0KDYACXX:7:2103:12093:12364_2:N:0:ATCACG A:96 100.00 101 0 0 1 101 829 729 1.2e-50 197.0 101
120
- HISEQ:151:C0KDYACXX:7:2104:15526:181864_2:N:0:ATCACG A:77 100.00 70 0 0 1 70 632 563 1.7e-32 137.0 70
121
- HISEQ:151:C0KDYACXX:7:2104:16103:188297_2:N:0:ATCACG A:73 100.00 101 0 0 1 101 652 752 1.6e-50 197.0 101
122
- HISEQ:151:C0KDYACXX:7:2105:11365:136970_2:N:0:ATCACG A:79 100.00 101 0 0 1 101 15 115 8.4e-51 198.0 101
123
- HISEQ:151:C0KDYACXX:7:2106:16833:56097_2:N:0:ATCACG A:94 100.00 99 0 0 1 99 1264 1166 1.3e-49 194.0 99
124
- HISEQ:151:C0KDYACXX:7:2107:6429:61313_2:N:0:ATCACG A:22 100.00 51 0 0 1 51 206 156 2.8e-21 100.0 51
125
- HISEQ:151:C0KDYACXX:7:2201:17229:87958_2:N:0:ATCACG A:48 100.00 101 0 0 1 101 273 173 1.4e-50 197.0 101
126
- HISEQ:151:C0KDYACXX:7:2201:6461:28885_2:N:0:ATCACG A:94 100.00 101 0 0 1 101 436 336 3.9e-51 199.0 101
127
- HISEQ:151:C0KDYACXX:7:2202:8852:183373_2:N:0:ATCACG A:81 100.00 101 0 0 1 101 71 171 1.1e-50 197.0 101
128
- HISEQ:151:C0KDYACXX:7:2204:1854:46040_2:N:0:ATCACG A:39 100.00 101 0 0 1 101 551 651 9.6e-51 198.0 101
129
- HISEQ:151:C0KDYACXX:7:2205:14128:144458_2:N:0:ATCACG A:78 100.00 101 0 0 1 101 1279 1179 2.3e-50 196.0 101
130
- HISEQ:151:C0KDYACXX:7:2205:2254:8730_2:N:0:ATCACG A:78 100.00 101 0 0 1 101 123 23 1.2e-50 197.0 101
131
- HISEQ:151:C0KDYACXX:7:2206:18099:79528_2:N:0:ATCACG A:28 100.00 101 0 0 1 101 1204 1104 2.1e-50 197.0 101
132
- HISEQ:151:C0KDYACXX:7:2206:20254:51010_2:N:0:ATCACG A:96 100.00 101 0 0 1 101 853 753 1.2e-50 197.0 101
133
- HISEQ:151:C0KDYACXX:7:2207:8535:15953_2:N:0:ATCACG A:64 100.00 101 0 0 1 101 1554 1454 1.4e-50 197.0 101
134
- HISEQ:151:C0KDYACXX:7:2207:9127:50806_2:N:0:ATCACG A:47 100.00 57 0 0 1 57 155 211 1.1e-24 111.0 57
135
- HISEQ:151:C0KDYACXX:7:2208:2650:62754_2:N:0:ATCACG A:90 100.00 100 0 0 1 100 135 234 1.1e-50 197.0 100
136
- HISEQ:151:C0KDYACXX:7:2302:17823:68484_2:N:0:ATCACG A:43 100.00 101 0 0 1 101 96 196 5.1e-51 199.0 101
137
- HISEQ:151:C0KDYACXX:7:2302:3190:158657_2:N:0:ATCACG A:37 100.00 101 0 0 1 101 352 452 5.1e-51 199.0 101
138
- HISEQ:151:C0KDYACXX:7:2303:16395:46079_2:N:0:ATCACG A:41 100.00 101 0 0 1 101 341 241 6.5e-51 198.0 101
139
- HISEQ:151:C0KDYACXX:7:2304:19722:197713_2:N:0:ATCACG A:63 100.00 60 0 0 1 60 2580 2521 1.5e-26 117.0 60
140
- HISEQ:151:C0KDYACXX:7:2304:6194:54369_2:N:0:ATCACG A:76 100.00 101 0 0 1 101 346 446 8.4e-51 198.0 101
141
- HISEQ:151:C0KDYACXX:7:2306:12653:190863_2:N:0:ATCACG A:95 98.89 90 1 0 1 90 203 114 1.6e-43 174.0 90
142
- HISEQ:151:C0KDYACXX:7:2306:5520:91514_2:N:0:ATCACG A:39 100.00 101 0 0 1 101 119 219 2.3e-50 196.0 101
143
- HISEQ:151:C0KDYACXX:7:2307:7316:188623_2:N:0:ATCACG A:95 100.00 69 0 0 1 69 202 134 3.7e-32 136.0 69
144
- HISEQ:151:C0KDYACXX:7:2308:16927:169908_2:N:0:ATCACG A:78 100.00 74 0 0 1 74 1205 1132 1.4e-34 144.0 74
145
- HISEQ:151:C0KDYACXX:7:2308:17989:87722_2:N:0:ATCACG A:45 100.00 101 0 0 1 101 621 721 1.2e-50 197.0 101
146
- HISEQ:151:C0KDYACXX:7:2308:8435:33639_2:N:0:ATCACG A:63 100.00 101 0 0 1 101 367 267 3.9e-51 199.0 101
147
- HISEQ:151:C0KDYACXX:7:1101:16202:38329_1:N:0:ATCACG A:73 100.00 101 0 0 1 101 927 1027 2.3e-50 196.0 101
148
- HISEQ:151:C0KDYACXX:7:1101:19844:33954_1:N:0:ATCACG A:64 100.00 91 0 0 1 91 170 260 7.5e-45 178.0 91
149
- HISEQ:151:C0KDYACXX:7:1101:3004:21994_1:N:0:ATCACG A:48 100.00 94 0 0 1 94 377 470 1.2e-46 184.0 94
150
- HISEQ:151:C0KDYACXX:7:1103:15132:135495_1:N:0:ATCACG A:94 100.00 101 0 0 1 101 894 994 4.4e-51 199.0 101
151
- HISEQ:151:C0KDYACXX:7:1103:15906:141721_1:N:0:ATCACG A:82 100.00 101 0 0 1 101 41 141 1.1e-50 197.0 101
152
- HISEQ:151:C0KDYACXX:7:1103:8939:53181_1:N:0:ATCACG A:79 100.00 101 0 0 1 101 377 277 2.3e-50 196.0 101
153
- HISEQ:151:C0KDYACXX:7:1105:10608:155657_1:N:0:ATCACG A:28 100.00 101 0 0 1 101 468 368 1.1e-50 197.0 101
154
- HISEQ:151:C0KDYACXX:7:1107:19864:151002_1:N:0:ATCACG A:48 100.00 101 0 0 1 101 453 353 9.6e-51 198.0 101
155
- HISEQ:151:C0KDYACXX:7:1107:2489:146485_1:N:0:ATCACG A:63 100.00 101 0 0 1 101 3539 3639 9.6e-51 198.0 101
156
- HISEQ:151:C0KDYACXX:7:1108:17848:102222_1:N:0:ATCACG A:96 100.00 101 0 0 1 101 608 708 5.1e-51 199.0 101
157
- HISEQ:151:C0KDYACXX:7:1201:10721:39206_1:N:0:ATCACG A:40 100.00 80 0 0 1 80 174 95 1.9e-38 157.0 80
158
- HISEQ:151:C0KDYACXX:7:1201:5349:152011_1:N:0:ATCACG A:84 98.11 53 1 0 1 53 1991 2043 4.9e-22 102.0 53
159
- HISEQ:151:C0KDYACXX:7:1201:7595:186741_1:N:0:ATCACG A:83 100.00 84 0 0 1 84 266 349 1.1e-40 164.0 84
160
- HISEQ:151:C0KDYACXX:7:1202:6857:15540_1:N:0:ATCACG A:58 100.00 101 0 0 1 101 308 408 3.4e-50 196.0 101
161
- HISEQ:151:C0KDYACXX:7:1204:18067:19236_1:N:0:ATCACG A:67 100.00 101 0 0 1 101 394 294 6.5e-51 198.0 101
162
- HISEQ:151:C0KDYACXX:7:1204:6118:187867_1:N:0:ATCACG A:71 100.00 101 0 0 1 101 2 102 5.1e-51 199.0 101
163
- HISEQ:151:C0KDYACXX:7:1206:9087:98837_1:N:0:ATCACG A:28 100.00 101 0 0 1 101 1707 1607 2.1e-50 197.0 101
164
- HISEQ:151:C0KDYACXX:7:1207:5718:150289_1:N:0:ATCACG A:65 100.00 101 0 0 1 101 137 37 3.0e-51 199.0 101
165
- HISEQ:151:C0KDYACXX:7:1208:12874:80128_1:N:0:ATCACG A:56 100.00 101 0 0 1 101 1545 1645 2.1e-50 197.0 101
166
- HISEQ:151:C0KDYACXX:7:1208:1562:39506_1:N:0:ATCACG A:96 100.00 100 0 0 1 100 487 388 1.8e-50 197.0 100
167
- HISEQ:151:C0KDYACXX:7:1301:14914:100746_1:N:0:ATCACG A:40 100.00 101 0 0 1 101 80 180 8.4e-51 198.0 101
168
- HISEQ:151:C0KDYACXX:7:1302:15971:106011_1:N:0:ATCACG A:90 100.00 101 0 0 1 101 153 53 5.7e-51 198.0 101
169
- HISEQ:151:C0KDYACXX:7:1302:7714:108638_1:N:0:ATCACG A:96 100.00 101 0 0 1 101 845 745 1.8e-50 197.0 101
170
- HISEQ:151:C0KDYACXX:7:1305:3344:109091_1:N:0:ATCACG A:19 100.00 101 0 0 1 101 718 618 2.7e-50 196.0 101
171
- HISEQ:151:C0KDYACXX:7:1307:20729:110819_1:N:0:ATCACG A:90 100.00 76 0 0 1 76 166 91 2.3e-36 150.0 76
172
- HISEQ:151:C0KDYACXX:7:1307:6419:64854_1:N:0:ATCACG A:63 100.00 79 0 0 1 79 3392 3314 6.0e-38 155.0 79
173
- HISEQ:151:C0KDYACXX:7:2103:11015:115457_1:N:0:ATCACG A:94 100.00 101 0 0 1 101 243 143 4.4e-51 199.0 101
174
- HISEQ:151:C0KDYACXX:7:2106:17893:25551_1:N:0:ATCACG A:30 100.00 101 0 0 1 101 690 790 1.4e-50 197.0 101
175
- HISEQ:151:C0KDYACXX:7:2106:20636:184898_1:N:0:ATCACG A:76 100.00 101 0 0 1 101 287 387 7.4e-51 198.0 101
176
- HISEQ:151:C0KDYACXX:7:2106:7454:176729_1:N:0:ATCACG A:25 100.00 72 0 0 1 72 780 709 2.1e-33 140.0 72
177
- HISEQ:151:C0KDYACXX:7:2107:17611:55528_1:N:0:ATCACG A:41 100.00 81 0 0 1 81 120 40 4.0e-39 159.0 81
178
- HISEQ:151:C0KDYACXX:7:2107:19384:32064_1:N:0:ATCACG A:28 98.99 99 1 0 1 99 1153 1055 5.7e-48 188.0 99
179
- HISEQ:151:C0KDYACXX:7:2107:8669:148977_1:N:0:ATCACG A:78 100.00 82 0 0 1 82 685 604 3.1e-39 159.0 82
180
- HISEQ:151:C0KDYACXX:7:2202:8013:169600_1:N:0:ATCACG A:86 100.00 101 0 0 1 101 3 103 1.1e-50 197.0 101
181
- HISEQ:151:C0KDYACXX:7:2202:8475:144641_1:N:0:ATCACG A:52 100.00 91 0 0 1 91 137 47 3.1e-45 179.0 91
182
- HISEQ:151:C0KDYACXX:7:2203:4645:73718_1:N:0:ATCACG A:71 100.00 101 0 0 1 101 822 722 1.4e-50 197.0 101
183
- HISEQ:151:C0KDYACXX:7:2204:12059:100238_1:N:0:ATCACG A:45 100.00 101 0 0 1 101 218 118 1.6e-50 197.0 101
184
- HISEQ:151:C0KDYACXX:7:2204:16638:50242_1:N:0:ATCACG A:65 100.00 101 0 0 1 101 1073 1173 9.6e-51 198.0 101
185
- HISEQ:151:C0KDYACXX:7:2204:3848:121242_1:N:0:ATCACG A:78 100.00 101 0 0 1 101 928 1028 1.6e-50 197.0 101
186
- HISEQ:151:C0KDYACXX:7:2205:18919:26390_1:N:0:ATCACG A:80 100.00 101 0 0 1 101 236 336 1.8e-50 197.0 101
187
- HISEQ:151:C0KDYACXX:7:2205:2385:172225_1:N:0:ATCACG A:2 100.00 101 0 0 1 101 228 328 6.5e-50 195.0 101
188
- HISEQ:151:C0KDYACXX:7:2206:12603:116452_1:N:0:ATCACG A:78 100.00 101 0 0 1 101 1235 1135 3.4e-50 196.0 101
189
- HISEQ:151:C0KDYACXX:7:2206:3206:140011_1:N:0:ATCACG A:63 100.00 58 0 0 1 58 682 739 2.0e-25 114.0 58
190
- HISEQ:151:C0KDYACXX:7:2208:11765:197858_1:N:0:ATCACG A:82 100.00 101 0 0 1 101 1000 900 8.4e-51 198.0 101
191
- HISEQ:151:C0KDYACXX:7:2302:15851:159703_1:N:0:ATCACG A:88 100.00 101 0 0 1 101 54 154 5.1e-51 199.0 101
192
- HISEQ:151:C0KDYACXX:7:2302:17559:53298_1:N:0:ATCACG A:82 100.00 101 0 0 1 101 195 95 9.6e-51 198.0 101
193
- HISEQ:151:C0KDYACXX:7:2305:7362:54262_1:N:0:ATCACG A:82 100.00 93 0 0 1 93 1346 1254 2.3e-46 183.0 93
194
- HISEQ:151:C0KDYACXX:7:2306:10685:174778_1:N:0:ATCACG A:41 100.00 100 0 0 1 100 38 137 3.5e-50 196.0 100
195
- HISEQ:151:C0KDYACXX:7:2306:4460:153541_1:N:0:ATCACG A:30 100.00 70 0 0 1 70 280 211 2.2e-32 137.0 70
196
- HISEQ:151:C0KDYACXX:7:2306:8343:175969_1:N:0:ATCACG A:31 100.00 101 0 0 1 101 1884 1784 1.2e-50 197.0 101
197
- HISEQ:151:C0KDYACXX:7:2307:17087:9140_1:N:0:ATCACG A:73 100.00 101 0 0 1 101 235 335 3.9e-50 196.0 101
198
- HISEQ:151:C0KDYACXX:7:2308:17547:20135_1:N:0:ATCACG A:84 100.00 101 0 0 1 101 596 496 7.4e-51 198.0 101
199
- HISEQ:151:C0KDYACXX:7:2308:5443:188377_1:N:0:ATCACG A:91 100.00 99 0 0 1 99 934 836 8.7e-50 194.0 99
200
- HISEQ:151:C0KDYACXX:7:1101:16202:38329_2:N:0:ATCACG A:73 100.00 101 0 0 1 101 938 838 1.8e-50 197.0 101
data/utils/enveomics/Tests/a_mg.reads-cds.counts.tsv DELETED
@@ -1,55 +0,0 @@
1
- A:8 5
2
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4
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7
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13
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14
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15
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16
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20
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22
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24
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26
- A:50 1
27
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28
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29
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30
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32
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33
- A:32 1
34
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40
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45
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47
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- A:74 3
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- A:84 7
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- A:82 6
data/utils/enveomics/Tests/alkB.nwk DELETED
@@ -1 +0,0 @@
1
- ((((((((gi|2623971|emb|CAA05333.1|:0.23647392926725346873,gi|5531221|emb|CAB51020.1|:0.02862387112111840909):0.33760291418751164905,(gi|13358856|dbj|BAB33287.1|:0.08119043667491317173,tr|B6Z2B2|B6Z2B2_9GAMM:0.20921720270120663931):0.42163623435556707442):0.31314482348247335564,(A-11148:0.37165984088130338270,((C-78859:0.08596919500451077889,gi|120325603|gb|ABM19918.1|:0.00000307626594619265):0.00000307626594619265,tr|B6Z2D5|B6Z2D5_MARHY:0.00928162414653887873):0.14826973350122188422):0.14775260948859672561):0.42030554056567270838,(((tr|B3U000|B3U000_9GAMM:0.05823540513729481838,(tr|B6Z2D0|B6Z2D0_9GAMM:0.14779070606581914959,(A-29995:0.00405607169666665542,B-38845:0.00000307626594619265):0.20568278550920432446):0.08679399567763973478):0.33544270916269791627,((G-61137:0.06016802608509013578,(B-25138:0.01114169843897101601,D-3317:0.00000307626594619265):0.12442854259772993808):0.22180310535394687221,((D-22801:0.00632969131290032992,G-162111:0.00000307626594619265):0.13454777689090618997,((tr|B6Z2B4|B6Z2B4_9GAMM:0.00000307626594619265,tr|B6Z2E5|B6Z2E5_9PROT:0.00000307626594619265):0.00000307626594619265,(tr|B6Z2B3|B6Z2B3_9BURK:0.01004128583511497939,tr|B6Z2A7|B6Z2A7_9GAMM:0.00000307626594619265):0.01004001780361192878):0.15691581678743679595):0.09628863992672781480):0.10711829818028278938):0.05447798275230692627,(tr|B6Z2A9|B6Z2A9_9GAMM:0.26376479080352688289,((B-35204:0.00000307626594619265,A-132156:0.00000307626594619265):0.00000307626594619265,C-70416:0.00000307626594619265):0.39637436017809807298):0.05966024489999132568):0.12944217664395935019):0.18857202508473755453,(((((((A-87946:14.38403874310352037469,tr|B6Z2D4|B6Z2D4_9BACI:0.00000307626594619265):0.04915833491335675626,tr|B6Z2A8|B6Z2A8_9GAMM:0.11309280768103933956):0.00000307626594619265,(tr|B6Z2E2|B6Z2E2_9GAMM:0.00000307626594619265,(tr|B6Z2A5|B6Z2A5_9GAMM:0.00000307626594619265,(tr|B0LCZ5|B0LCZ5_9GAMM:0.00000307626594619265,tr|B6Z298|B6Z298_9GAMM:0.00000307626594619265):0.00000307626594619265):0.00000307626594619265):0.00000307626594619265):0.00000307626594619265,(tr|B6Z292|B6Z292_9MICO:0.00000307626594619265,tr|B6Z2D2|B6Z2D2_9GAMM:0.00000307626594619265):0.00975582823471030959):0.37093052837760032148,((tr|B6Z2B1|B6Z2B1_9GAMM:0.01080252232446939943,(A-21483:0.00000307626594619265,B-22100:0.00000307626594619265):0.03099250019684049451):0.17874969201523729923,(tr|B6Z2D7|B6Z2D7_9GAMM:0.07541431239328290348,(((tr|B6Z2A0|B6Z2A0_9GAMM:0.00000307626594619265,(tr|B6Z293|B6Z293_9GAMM:0.00000307626594619265,(((tr|B6Z2D1|B6Z2D1_9GAMM:0.00000307626594619265,tr|B6Z2A3|B6Z2A3_9MICO:0.00000307626594619265):0.00000307626594619265,tr|B6Z2D6|B6Z2D6_9GAMM:0.00000307626594619265):0.00000307626594619265,tr|B6Z296|B6Z296_9GAMM:0.00000307626594619265):0.00000307626594619265):0.00000307626594619265):0.00000307626594619265,(tr|B6Z2D9|B6Z2D9_9GAMM:0.00000307626594619265,((tr|B6Z2A2|B6Z2A2_9BACI:0.00000307626594619265,tr|B6Z291|B6Z291_9MICO:0.00000307626594619265):0.00000307626594619265,tr|B6Z290|B6Z290_9GAMM:0.00000307626594619265):0.00000307626594619265):0.00000307626594619265):0.00000307626594619265,(tr|B6Z2E3|B6Z2E3_9GAMM:0.02032548150409536902,tr|B6Z299|B6Z299_9GAMM:0.49740753476171112313):0.00000307626594619265):0.06402970820406528318):0.08471029664109464008):0.31386186762792450677):0.23389359968645995203,(((S4-22309:0.32088942924443997207,(S4-6072:0.00000307626594619265,S3-5250:0.00000307626594619265):0.25879274851195993579):0.26885336260486530913,((((G-36873:0.00000307626594619265,A-13753:0.00000307626594619265):0.00000307626594619265,B-41998:0.00000307626594619265):0.35060649887378608769,(S4-23470:0.00000307626594619265,S3-8321:0.00766444906061485368):0.56101384414434085635):0.14729485658596505604,S4-11063:0.70334497370743109812):0.04835217504685293544):0.16975586666904743383,((gi|5531405|emb|CAB51047.1|:0.23742974535279914861,(((((tr|B6Z2B7|B6Z2B7_9GAMM:0.00000307626594619265,tr|B6Z284|B6Z284_9GAMM:0.00000307626594619265):0.00000307626594619265,tr|B6Z2D8|B6Z2D8_9GAMM:0.00000307626594619265):0.00952984231030562165,(gi|37360912|dbj|BAC98365.1|:0.00283379156405169337,gi|13992203|emb|CAC38027.1|:0.00000307626594619265):0.00000307626594619265):0.13832554734898203086,(((B-27295:0.03163938335823503201,A-15789:0.00000307626594619265):0.00000307626594619265,tr|C7DLJ8|C7DLJ8_9ALTE:0.00000307626594619265):0.01323795912440724198,(gi|120323226|gb|ABM17541.1|:0.00733233844092330816,C-45126:0.02297338043741844679):0.00000307626594619265):0.05446825134922440859):0.09736929720609276140,(A-92019:0.02963015149053232003,(tr|B6Z2E4|B6Z2E4_9PROT:0.00968838549699064730,(G-159976:0.00000307626594619265,(((E-7971:0.00000307626594619265,C-21170:0.00000307626594619265):0.00000307626594619265,B-114387:0.00000307626594619265):0.00000307626594619265,F-76495:0.00000307626594619265):0.00000307626594619265):0.00000307626594619265):0.03797586760545500900):0.14756568068187181364):0.06397665460931205306):0.12150410950118115117,gi|18996281|emb|CAD24434.1|:0.27065752895112665799):0.42339727456335563005):0.05655629112615628146):0.40856666165556260184,((tr|B6Z2E1|B6Z2E1_9GAMM:0.18554394906222618222,(tr|B6Z2B0|B6Z2B0_9GAMM:0.01886376887616230194,(tr|B6Z2A6|B6Z2A6_9GAMM:0.00000307626594619265,tr|B6Z294|B6Z294_9GAMM:0.01873801435647269933):0.00000307626594619265):0.09563400821490432302):0.23842348383791245325,(gi|54016798|dbj|BAD58168.1|:0.61869044344623747023,(gi|54018099|dbj|BAD59469.1|:0.34545981498528061104,(tr|Q5WA49|Q5WA49_9ACTO:0.02654543622722535870,tr|C7DLJ7|C7DLJ7_9ACTO:0.03775873865566014426):0.24565450355334780830):0.22118933613665645033):0.15160688902578120518):0.11176566950974699266):0.07177729143117751731):0.07126876639790918899,((((A-22280:0.29944887487557814154,A-122322:0.11510404866941430224):9.40368377911436503780,tr|Q9XAV1|Q9XAV1_PSEFL:0.10804533858196024854):0.47024346425452545617,(((tr|B6Z295|B6Z295_9MICO:0.17377532808816989474,tr|B6Z2B8|B6Z2B8_9GAMM:0.09204640243146197665):0.07753840297364610057,(tr|A7LAC3|A7LAC3_9GAMM:0.00000307626594619265,(tr|B6Z2A4|B6Z2A4_9GAMM:0.00000307626594619265,gi|270309099|gb|AAT91722.2|:0.00000307626594619265):0.05073140986745830472):0.14879909834895560516):0.03654295104942567596,tr|Q6B433|Q6B433_9GAMM:0.07552545591341504327):0.15824217496745546230):0.10176231199734972477,tr|Q9AEN3|Q9AEN3_BURCE:0.43025449556767880743):0.12047115354506787721):0.47534635843090700114,(((B-104580:0.20027185713913028819,(C-33435:0.00395329974141714335,A-105931:0.00000307626594619265):0.31731540868684887657):0.18883926988103255651,((B-59514:0.32289114784668604408,((D-46790:0.05809052473454456161,((gi|33186770|emb|CAE17295.1|:0.00000307626594619265,gi|37360914|dbj|BAC98366.1|:0.00000307626594619265):0.00000307626594619265,tr|B6Z2C9|B6Z2C9_9GAMM:0.00000307626594619265):0.05112927444701064611):0.08887147604051320871,A-22278:0.14892145984465848807):0.38455429817142178228):0.15505236345226111605,(A-122070:0.42873920948105842532,(gi|9948635|gb|AAG05962.1|AE004685_8:0.39625896395294829544,gi|9947483|gb|AAG04914.1|AE004581_1:0.41923936845025072673):0.15200172554195354180):0.15426169871085021468):0.11912696938956793269):0.25537607873837275818,S2-11245:0.68413832140684327499):0.46663559492070949553):2.26257672914658281016,gi|139854|sp|P21395.1|XYLM_PSEPU:2.26257672914658281016);
data/utils/enveomics/Tests/anthrax-cansnp-data.tsv DELETED
@@ -1,13 +0,0 @@
1
- Lineage Type strain Sequence A.Br.001 A.Br.002 A.Br.003 A.Br.004 A.Br.006 A.Br.007 A.Br.008 A.Br.009 B.Br.001 B.Br.002 B.Br.003 B.Br.004 A/B.Br.001
2
- C.Br.A1055 C.A1055 C.USA.A1055 T G A T C T T A T G G T G
3
- B.Br.KrugerB B1.A0442 KrugerB T G A T C T T A C T A T A
4
- B.Br.001/002 B1.A0102 T G A T C T T A T T A T A
5
- B.Br.CNEVA B2.A0402 CNEVA.9066 T G A T C T T A T G A C A
6
- A.Br.Ames A2.A0462 Ames C A G C A T T A T G G T A
7
- A.Br.001/002 A2.A0034 T A G C A T T A T G G T A
8
- A.Br.Aust94 A1.A0039 Australia94 T G G C A T T A T G G T A
9
- A.Br.003/004 A2.A0489 T G A C A T T A T G G T A
10
- A.Br.Vollum A1.A0488 Vollum T G A T A C T A T G G T A
11
- A.Br.005/006 A1.A0158 T G A T A T T A T G G T A
12
- A.Br.008/009 A1.A0293 T G A T A T G A T G G T A
13
- A.Br.WNA A1.A0193 W. N. America T G A T A T G G T G G T A
data/utils/enveomics/Tests/anthrax-cansnp-key.tsv DELETED
@@ -1,17 +0,0 @@
1
- # C group
2
- 1 A/B.Br.001 G:C.Br.A1055 A:[2]
3
- # A/B groups
4
- 2 B.Br.003 A:[3] G:[6]
5
- # B group
6
- 3 B.Br.004 C:B.Br.CNEVA T:[4]
7
- 4 B.Br.002 G:B.Br.002/003 T:[5]
8
- 5 B.Br.001 C:B.Br.KrugerB T:B.Br.001/002
9
- # A group
10
- 6 A.Br.006 C:A.Br.006/root A:[7]
11
- 7 A.Br.007 C:A.Br.Vollum T:[8]
12
- 8 A.Br.004 T:[12] C:[9]
13
- 9 A.Br.003 A:A.Br.003/004 G:[10]
14
- 10 A.Br.002 G:A.Br.Aust94 A:[11]
15
- 11 A.Br.001 C:A.Br.Ames T:A.Br.001/002
16
- 12 A.Br.008 T:A.Br.008/005 G:[13]
17
- 13 A.Br.009 G:A.Br.WNA A:A.Br.008/009