miga-base 0.7.26.0 → 1.0.0.1

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 (337) hide show
  1. checksums.yaml +4 -4
  2. data/lib/miga/_data/aai-intax.blast.tsv.gz +0 -0
  3. data/lib/miga/_data/aai-intax.diamond.tsv.gz +0 -0
  4. data/lib/miga/_data/aai-novel.blast.tsv.gz +0 -0
  5. data/lib/miga/_data/aai-novel.diamond.tsv.gz +0 -0
  6. data/lib/miga/cli/action/classify_wf.rb +2 -2
  7. data/lib/miga/cli/action/derep_wf.rb +1 -1
  8. data/lib/miga/cli/action/doctor.rb +57 -14
  9. data/lib/miga/cli/action/doctor/base.rb +47 -23
  10. data/lib/miga/cli/action/init.rb +11 -7
  11. data/lib/miga/cli/action/init/files_helper.rb +1 -0
  12. data/lib/miga/cli/action/ncbi_get.rb +3 -3
  13. data/lib/miga/cli/action/tax_dist.rb +2 -2
  14. data/lib/miga/cli/action/wf.rb +5 -4
  15. data/lib/miga/common.rb +1 -0
  16. data/lib/miga/daemon.rb +11 -4
  17. data/lib/miga/dataset/result.rb +10 -6
  18. data/lib/miga/json.rb +5 -4
  19. data/lib/miga/metadata.rb +5 -1
  20. data/lib/miga/parallel.rb +36 -0
  21. data/lib/miga/project.rb +8 -8
  22. data/lib/miga/project/base.rb +4 -4
  23. data/lib/miga/project/result.rb +2 -2
  24. data/lib/miga/sqlite.rb +10 -2
  25. data/lib/miga/version.rb +23 -9
  26. data/scripts/aai_distances.bash +16 -18
  27. data/scripts/ani_distances.bash +16 -17
  28. data/scripts/assembly.bash +31 -16
  29. data/scripts/haai_distances.bash +3 -27
  30. data/scripts/miga.bash +6 -4
  31. data/scripts/p.bash +1 -1
  32. data/scripts/read_quality.bash +9 -18
  33. data/scripts/trimmed_fasta.bash +14 -30
  34. data/scripts/trimmed_reads.bash +36 -36
  35. data/test/parallel_test.rb +31 -0
  36. data/test/project_test.rb +2 -1
  37. data/test/remote_dataset_test.rb +1 -1
  38. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Archaea_SCG.hmm +41964 -0
  39. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Bacteria_SCG.hmm +32439 -0
  40. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Complete_SCG_DB.hmm +62056 -0
  41. data/utils/FastAAI/FastAAI/FastAAI +1336 -0
  42. data/utils/FastAAI/README.md +84 -0
  43. data/utils/FastAAI/kAAI_v1.0_virus.py +1296 -0
  44. data/utils/distance/commands.rb +1 -0
  45. data/utils/distance/database.rb +0 -1
  46. data/utils/distance/runner.rb +2 -4
  47. data/utils/enveomics/Docs/recplot2.md +244 -0
  48. data/utils/enveomics/Examples/aai-matrix.bash +66 -0
  49. data/utils/enveomics/Examples/ani-matrix.bash +66 -0
  50. data/utils/enveomics/Examples/essential-phylogeny.bash +105 -0
  51. data/utils/enveomics/Examples/unus-genome-phylogeny.bash +100 -0
  52. data/utils/enveomics/LICENSE.txt +73 -0
  53. data/utils/enveomics/Makefile +52 -0
  54. data/utils/enveomics/Manifest/Tasks/aasubs.json +103 -0
  55. data/utils/enveomics/Manifest/Tasks/blasttab.json +786 -0
  56. data/utils/enveomics/Manifest/Tasks/distances.json +161 -0
  57. data/utils/enveomics/Manifest/Tasks/fasta.json +802 -0
  58. data/utils/enveomics/Manifest/Tasks/fastq.json +291 -0
  59. data/utils/enveomics/Manifest/Tasks/graphics.json +126 -0
  60. data/utils/enveomics/Manifest/Tasks/mapping.json +137 -0
  61. data/utils/enveomics/Manifest/Tasks/ogs.json +382 -0
  62. data/utils/enveomics/Manifest/Tasks/other.json +906 -0
  63. data/utils/enveomics/Manifest/Tasks/remote.json +355 -0
  64. data/utils/enveomics/Manifest/Tasks/sequence-identity.json +638 -0
  65. data/utils/enveomics/Manifest/Tasks/tables.json +308 -0
  66. data/utils/enveomics/Manifest/Tasks/trees.json +68 -0
  67. data/utils/enveomics/Manifest/Tasks/variants.json +111 -0
  68. data/utils/enveomics/Manifest/categories.json +165 -0
  69. data/utils/enveomics/Manifest/examples.json +154 -0
  70. data/utils/enveomics/Manifest/tasks.json +4 -0
  71. data/utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash +69 -0
  72. data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +1 -0
  73. data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +1 -0
  74. data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +1 -0
  75. data/utils/enveomics/Pipelines/assembly.pbs/README.md +189 -0
  76. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash +112 -0
  77. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash +23 -0
  78. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash +44 -0
  79. data/utils/enveomics/Pipelines/assembly.pbs/RUNME.bash +50 -0
  80. data/utils/enveomics/Pipelines/assembly.pbs/kSelector.R +37 -0
  81. data/utils/enveomics/Pipelines/assembly.pbs/newbler.pbs +68 -0
  82. data/utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl +49 -0
  83. data/utils/enveomics/Pipelines/assembly.pbs/soap.pbs +80 -0
  84. data/utils/enveomics/Pipelines/assembly.pbs/stats.pbs +57 -0
  85. data/utils/enveomics/Pipelines/assembly.pbs/velvet.pbs +63 -0
  86. data/utils/enveomics/Pipelines/blast.pbs/01.pbs.bash +38 -0
  87. data/utils/enveomics/Pipelines/blast.pbs/02.pbs.bash +73 -0
  88. data/utils/enveomics/Pipelines/blast.pbs/03.pbs.bash +21 -0
  89. data/utils/enveomics/Pipelines/blast.pbs/BlastTab.recover_job.pl +72 -0
  90. data/utils/enveomics/Pipelines/blast.pbs/CONFIG.mock.bash +98 -0
  91. data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +1 -0
  92. data/utils/enveomics/Pipelines/blast.pbs/README.md +127 -0
  93. data/utils/enveomics/Pipelines/blast.pbs/RUNME.bash +109 -0
  94. data/utils/enveomics/Pipelines/blast.pbs/TASK.check.bash +128 -0
  95. data/utils/enveomics/Pipelines/blast.pbs/TASK.dry.bash +16 -0
  96. data/utils/enveomics/Pipelines/blast.pbs/TASK.eo.bash +22 -0
  97. data/utils/enveomics/Pipelines/blast.pbs/TASK.pause.bash +26 -0
  98. data/utils/enveomics/Pipelines/blast.pbs/TASK.run.bash +89 -0
  99. data/utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash +29 -0
  100. data/utils/enveomics/Pipelines/idba.pbs/README.md +49 -0
  101. data/utils/enveomics/Pipelines/idba.pbs/RUNME.bash +95 -0
  102. data/utils/enveomics/Pipelines/idba.pbs/run.pbs +56 -0
  103. data/utils/enveomics/Pipelines/trim.pbs/README.md +54 -0
  104. data/utils/enveomics/Pipelines/trim.pbs/RUNME.bash +70 -0
  105. data/utils/enveomics/Pipelines/trim.pbs/run.pbs +130 -0
  106. data/utils/enveomics/README.md +42 -0
  107. data/utils/enveomics/Scripts/AAsubs.log2ratio.rb +171 -0
  108. data/utils/enveomics/Scripts/Aln.cat.rb +221 -0
  109. data/utils/enveomics/Scripts/Aln.convert.pl +35 -0
  110. data/utils/enveomics/Scripts/AlphaDiversity.pl +152 -0
  111. data/utils/enveomics/Scripts/BedGraph.tad.rb +93 -0
  112. data/utils/enveomics/Scripts/BedGraph.window.rb +71 -0
  113. data/utils/enveomics/Scripts/BlastPairwise.AAsubs.pl +102 -0
  114. data/utils/enveomics/Scripts/BlastTab.addlen.rb +63 -0
  115. data/utils/enveomics/Scripts/BlastTab.advance.bash +48 -0
  116. data/utils/enveomics/Scripts/BlastTab.best_hit_sorted.pl +55 -0
  117. data/utils/enveomics/Scripts/BlastTab.catsbj.pl +104 -0
  118. data/utils/enveomics/Scripts/BlastTab.cogCat.rb +76 -0
  119. data/utils/enveomics/Scripts/BlastTab.filter.pl +47 -0
  120. data/utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl +194 -0
  121. data/utils/enveomics/Scripts/BlastTab.metaxaPrep.pl +104 -0
  122. data/utils/enveomics/Scripts/BlastTab.pairedHits.rb +157 -0
  123. data/utils/enveomics/Scripts/BlastTab.recplot2.R +48 -0
  124. data/utils/enveomics/Scripts/BlastTab.seqdepth.pl +86 -0
  125. data/utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl +119 -0
  126. data/utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl +86 -0
  127. data/utils/enveomics/Scripts/BlastTab.subsample.pl +47 -0
  128. data/utils/enveomics/Scripts/BlastTab.sumPerHit.pl +114 -0
  129. data/utils/enveomics/Scripts/BlastTab.taxid2taxrank.pl +90 -0
  130. data/utils/enveomics/Scripts/BlastTab.topHits_sorted.rb +101 -0
  131. data/utils/enveomics/Scripts/Chao1.pl +97 -0
  132. data/utils/enveomics/Scripts/CharTable.classify.rb +234 -0
  133. data/utils/enveomics/Scripts/EBIseq2tax.rb +83 -0
  134. data/utils/enveomics/Scripts/FastA.N50.pl +60 -0
  135. data/utils/enveomics/Scripts/FastA.extract.rb +152 -0
  136. data/utils/enveomics/Scripts/FastA.filter.pl +52 -0
  137. data/utils/enveomics/Scripts/FastA.filterLen.pl +28 -0
  138. data/utils/enveomics/Scripts/FastA.filterN.pl +60 -0
  139. data/utils/enveomics/Scripts/FastA.fragment.rb +100 -0
  140. data/utils/enveomics/Scripts/FastA.gc.pl +42 -0
  141. data/utils/enveomics/Scripts/FastA.interpose.pl +93 -0
  142. data/utils/enveomics/Scripts/FastA.length.pl +38 -0
  143. data/utils/enveomics/Scripts/FastA.mask.rb +89 -0
  144. data/utils/enveomics/Scripts/FastA.per_file.pl +36 -0
  145. data/utils/enveomics/Scripts/FastA.qlen.pl +57 -0
  146. data/utils/enveomics/Scripts/FastA.rename.pl +65 -0
  147. data/utils/enveomics/Scripts/FastA.revcom.pl +23 -0
  148. data/utils/enveomics/Scripts/FastA.sample.rb +98 -0
  149. data/utils/enveomics/Scripts/FastA.slider.pl +85 -0
  150. data/utils/enveomics/Scripts/FastA.split.pl +55 -0
  151. data/utils/enveomics/Scripts/FastA.split.rb +79 -0
  152. data/utils/enveomics/Scripts/FastA.subsample.pl +131 -0
  153. data/utils/enveomics/Scripts/FastA.tag.rb +65 -0
  154. data/utils/enveomics/Scripts/FastA.toFastQ.rb +69 -0
  155. data/utils/enveomics/Scripts/FastA.wrap.rb +48 -0
  156. data/utils/enveomics/Scripts/FastQ.filter.pl +54 -0
  157. data/utils/enveomics/Scripts/FastQ.interpose.pl +90 -0
  158. data/utils/enveomics/Scripts/FastQ.maskQual.rb +89 -0
  159. data/utils/enveomics/Scripts/FastQ.offset.pl +90 -0
  160. data/utils/enveomics/Scripts/FastQ.split.pl +53 -0
  161. data/utils/enveomics/Scripts/FastQ.tag.rb +70 -0
  162. data/utils/enveomics/Scripts/FastQ.test-error.rb +81 -0
  163. data/utils/enveomics/Scripts/FastQ.toFastA.awk +24 -0
  164. data/utils/enveomics/Scripts/GFF.catsbj.pl +127 -0
  165. data/utils/enveomics/Scripts/GenBank.add_fields.rb +84 -0
  166. data/utils/enveomics/Scripts/HMM.essential.rb +351 -0
  167. data/utils/enveomics/Scripts/HMM.haai.rb +168 -0
  168. data/utils/enveomics/Scripts/HMMsearch.extractIds.rb +83 -0
  169. data/utils/enveomics/Scripts/JPlace.distances.rb +88 -0
  170. data/utils/enveomics/Scripts/JPlace.to_iToL.rb +320 -0
  171. data/utils/enveomics/Scripts/M5nr.getSequences.rb +81 -0
  172. data/utils/enveomics/Scripts/MeTaxa.distribution.pl +198 -0
  173. data/utils/enveomics/Scripts/MyTaxa.fragsByTax.pl +35 -0
  174. data/utils/enveomics/Scripts/MyTaxa.seq-taxrank.rb +49 -0
  175. data/utils/enveomics/Scripts/NCBIacc2tax.rb +92 -0
  176. data/utils/enveomics/Scripts/Newick.autoprune.R +27 -0
  177. data/utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl +228 -0
  178. data/utils/enveomics/Scripts/RecPlot2.compareIdentities.R +32 -0
  179. data/utils/enveomics/Scripts/RefSeq.download.bash +48 -0
  180. data/utils/enveomics/Scripts/SRA.download.bash +55 -0
  181. data/utils/enveomics/Scripts/TRIBS.plot-test.R +36 -0
  182. data/utils/enveomics/Scripts/TRIBS.test.R +39 -0
  183. data/utils/enveomics/Scripts/Table.barplot.R +31 -0
  184. data/utils/enveomics/Scripts/Table.df2dist.R +30 -0
  185. data/utils/enveomics/Scripts/Table.filter.pl +61 -0
  186. data/utils/enveomics/Scripts/Table.merge.pl +77 -0
  187. data/utils/enveomics/Scripts/Table.prefScore.R +60 -0
  188. data/utils/enveomics/Scripts/Table.replace.rb +69 -0
  189. data/utils/enveomics/Scripts/Table.round.rb +63 -0
  190. data/utils/enveomics/Scripts/Table.split.pl +57 -0
  191. data/utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb +227 -0
  192. data/utils/enveomics/Scripts/VCF.KaKs.rb +147 -0
  193. data/utils/enveomics/Scripts/VCF.SNPs.rb +88 -0
  194. data/utils/enveomics/Scripts/aai.rb +419 -0
  195. data/utils/enveomics/Scripts/ani.rb +362 -0
  196. data/utils/enveomics/Scripts/anir.rb +137 -0
  197. data/utils/enveomics/Scripts/clust.rand.rb +102 -0
  198. data/utils/enveomics/Scripts/gi2tax.rb +103 -0
  199. data/utils/enveomics/Scripts/in_silico_GA_GI.pl +96 -0
  200. data/utils/enveomics/Scripts/lib/data/dupont_2012_essential.hmm.gz +0 -0
  201. data/utils/enveomics/Scripts/lib/data/lee_2019_essential.hmm.gz +0 -0
  202. data/utils/enveomics/Scripts/lib/enveomics.R +1 -0
  203. data/utils/enveomics/Scripts/lib/enveomics_rb/anir.rb +293 -0
  204. data/utils/enveomics/Scripts/lib/enveomics_rb/bm_set.rb +175 -0
  205. data/utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb +24 -0
  206. data/utils/enveomics/Scripts/lib/enveomics_rb/errors.rb +17 -0
  207. data/utils/enveomics/Scripts/lib/enveomics_rb/gmm_em.rb +30 -0
  208. data/utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb +253 -0
  209. data/utils/enveomics/Scripts/lib/enveomics_rb/match.rb +63 -0
  210. data/utils/enveomics/Scripts/lib/enveomics_rb/og.rb +182 -0
  211. data/utils/enveomics/Scripts/lib/enveomics_rb/rbm.rb +49 -0
  212. data/utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb +74 -0
  213. data/utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb +237 -0
  214. data/utils/enveomics/Scripts/lib/enveomics_rb/stats.rb +3 -0
  215. data/utils/enveomics/Scripts/lib/enveomics_rb/stats/rand.rb +31 -0
  216. data/utils/enveomics/Scripts/lib/enveomics_rb/stats/sample.rb +152 -0
  217. data/utils/enveomics/Scripts/lib/enveomics_rb/utils.rb +73 -0
  218. data/utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb +135 -0
  219. data/utils/enveomics/Scripts/ogs.annotate.rb +88 -0
  220. data/utils/enveomics/Scripts/ogs.core-pan.rb +160 -0
  221. data/utils/enveomics/Scripts/ogs.extract.rb +125 -0
  222. data/utils/enveomics/Scripts/ogs.mcl.rb +186 -0
  223. data/utils/enveomics/Scripts/ogs.rb +104 -0
  224. data/utils/enveomics/Scripts/ogs.stats.rb +131 -0
  225. data/utils/enveomics/Scripts/rbm-legacy.rb +172 -0
  226. data/utils/enveomics/Scripts/rbm.rb +100 -0
  227. data/utils/enveomics/Scripts/sam.filter.rb +148 -0
  228. data/utils/enveomics/Tests/Makefile +10 -0
  229. data/utils/enveomics/Tests/Mgen_M2288.faa +3189 -0
  230. data/utils/enveomics/Tests/Mgen_M2288.fna +8282 -0
  231. data/utils/enveomics/Tests/Mgen_M2321.fna +8288 -0
  232. data/utils/enveomics/Tests/Nequ_Kin4M.faa +2970 -0
  233. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata +0 -0
  234. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt +7 -0
  235. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv +17 -0
  236. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv +137 -0
  237. data/utils/enveomics/Tests/a_mg.cds-go.blast.tsv +123 -0
  238. data/utils/enveomics/Tests/a_mg.reads-cds.blast.tsv +200 -0
  239. data/utils/enveomics/Tests/a_mg.reads-cds.counts.tsv +55 -0
  240. data/utils/enveomics/Tests/alkB.nwk +1 -0
  241. data/utils/enveomics/Tests/anthrax-cansnp-data.tsv +13 -0
  242. data/utils/enveomics/Tests/anthrax-cansnp-key.tsv +17 -0
  243. data/utils/enveomics/Tests/hiv1.faa +59 -0
  244. data/utils/enveomics/Tests/hiv1.fna +134 -0
  245. data/utils/enveomics/Tests/hiv2.faa +70 -0
  246. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv +233 -0
  247. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim +1 -0
  248. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec +233 -0
  249. data/utils/enveomics/Tests/phyla_counts.tsv +10 -0
  250. data/utils/enveomics/Tests/primate_lentivirus.ogs +11 -0
  251. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm +9 -0
  252. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm +8 -0
  253. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm +6 -0
  254. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm +9 -0
  255. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm +6 -0
  256. data/utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm +6 -0
  257. data/utils/enveomics/build_enveomics_r.bash +45 -0
  258. data/utils/enveomics/enveomics.R/DESCRIPTION +31 -0
  259. data/utils/enveomics/enveomics.R/NAMESPACE +39 -0
  260. data/utils/enveomics/enveomics.R/R/autoprune.R +155 -0
  261. data/utils/enveomics/enveomics.R/R/barplot.R +184 -0
  262. data/utils/enveomics/enveomics.R/R/cliopts.R +135 -0
  263. data/utils/enveomics/enveomics.R/R/df2dist.R +154 -0
  264. data/utils/enveomics/enveomics.R/R/growthcurve.R +331 -0
  265. data/utils/enveomics/enveomics.R/R/prefscore.R +79 -0
  266. data/utils/enveomics/enveomics.R/R/recplot.R +354 -0
  267. data/utils/enveomics/enveomics.R/R/recplot2.R +1631 -0
  268. data/utils/enveomics/enveomics.R/R/tribs.R +583 -0
  269. data/utils/enveomics/enveomics.R/R/utils.R +80 -0
  270. data/utils/enveomics/enveomics.R/README.md +81 -0
  271. data/utils/enveomics/enveomics.R/data/growth.curves.rda +0 -0
  272. data/utils/enveomics/enveomics.R/data/phyla.counts.rda +0 -0
  273. data/utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd +16 -0
  274. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd +16 -0
  275. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd +16 -0
  276. data/utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd +25 -0
  277. data/utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd +46 -0
  278. data/utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd +23 -0
  279. data/utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd +47 -0
  280. data/utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd +23 -0
  281. data/utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd +23 -0
  282. data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd +40 -0
  283. data/utils/enveomics/enveomics.R/man/enve.barplot.Rd +103 -0
  284. data/utils/enveomics/enveomics.R/man/enve.cliopts.Rd +67 -0
  285. data/utils/enveomics/enveomics.R/man/enve.col.alpha.Rd +24 -0
  286. data/utils/enveomics/enveomics.R/man/enve.col2alpha.Rd +19 -0
  287. data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd +45 -0
  288. data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd +44 -0
  289. data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd +47 -0
  290. data/utils/enveomics/enveomics.R/man/enve.growthcurve.Rd +75 -0
  291. data/utils/enveomics/enveomics.R/man/enve.prefscore.Rd +50 -0
  292. data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd +44 -0
  293. data/utils/enveomics/enveomics.R/man/enve.recplot.Rd +139 -0
  294. data/utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd +45 -0
  295. data/utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd +24 -0
  296. data/utils/enveomics/enveomics.R/man/enve.recplot2.Rd +77 -0
  297. data/utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd +25 -0
  298. data/utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd +21 -0
  299. data/utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd +19 -0
  300. data/utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd +19 -0
  301. data/utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd +47 -0
  302. data/utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd +29 -0
  303. data/utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd +18 -0
  304. data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd +45 -0
  305. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd +36 -0
  306. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd +19 -0
  307. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd +19 -0
  308. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd +27 -0
  309. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd +52 -0
  310. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd +17 -0
  311. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd +51 -0
  312. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd +43 -0
  313. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd +82 -0
  314. data/utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd +59 -0
  315. data/utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd +27 -0
  316. data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd +36 -0
  317. data/utils/enveomics/enveomics.R/man/enve.selvector.Rd +23 -0
  318. data/utils/enveomics/enveomics.R/man/enve.tribs.Rd +68 -0
  319. data/utils/enveomics/enveomics.R/man/enve.tribs.test.Rd +28 -0
  320. data/utils/enveomics/enveomics.R/man/enve.truncate.Rd +27 -0
  321. data/utils/enveomics/enveomics.R/man/growth.curves.Rd +14 -0
  322. data/utils/enveomics/enveomics.R/man/phyla.counts.Rd +13 -0
  323. data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd +78 -0
  324. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd +46 -0
  325. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd +45 -0
  326. data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd +125 -0
  327. data/utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd +19 -0
  328. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd +19 -0
  329. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd +19 -0
  330. data/utils/enveomics/globals.mk +8 -0
  331. data/utils/enveomics/manifest.json +9 -0
  332. data/utils/multitrim/Multitrim How-To.pdf +0 -0
  333. data/utils/multitrim/README.md +67 -0
  334. data/utils/multitrim/multitrim.py +1555 -0
  335. data/utils/multitrim/multitrim.yml +13 -0
  336. data/utils/requirements.txt +4 -3
  337. metadata +304 -3
data/utils/enveomics/Tests/a_mg.reads-cds.counts.tsv ADDED
@@ -0,0 +1,55 @@
1
+ A:8 5
2
+ A:65 7
3
+ A:53 3
4
+ A:6 1
5
+ A:41 5
6
+ A:18 1
7
+ A:91 3
8
+ A:52 1
9
+ A:40 5
10
+ A:78 10
11
+ A:83 3
12
+ A:94 12
13
+ A:95 2
14
+ A:49 1
15
+ A:35 3
16
+ A:45 3
17
+ A:63 9
18
+ A:7 2
19
+ A:88 1
20
+ A:28 8
21
+ A:77 3
22
+ A:47 3
23
+ A:48 6
24
+ A:31 3
25
+ A:25 1
26
+ A:50 1
27
+ A:81 7
28
+ A:56 6
29
+ A:86 1
30
+ A:71 3
31
+ A:22 1
32
+ A:67 1
33
+ A:32 1
34
+ A:76 5
35
+ A:90 3
36
+ A:58 1
37
+ A:72 2
38
+ A:30 2
39
+ A:64 8
40
+ A:79 4
41
+ A:37 3
42
+ A:9 1
43
+ A:57 1
44
+ A:97 1
45
+ A:96 5
46
+ A:80 1
47
+ A:73 8
48
+ A:14 1
49
+ A:43 6
50
+ A:19 5
51
+ A:74 3
52
+ A:39 4
53
+ A:2 1
54
+ A:84 7
55
+ A:82 6
data/utils/enveomics/Tests/alkB.nwk ADDED
@@ -0,0 +1 @@
1
+ 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data/utils/enveomics/Tests/anthrax-cansnp-data.tsv ADDED
@@ -0,0 +1,13 @@
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 ADDED
@@ -0,0 +1,17 @@
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
data/utils/enveomics/Tests/hiv1.faa ADDED
@@ -0,0 +1,59 @@
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 ADDED
@@ -0,0 +1,134 @@
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 ADDED
@@ -0,0 +1,70 @@
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 ADDED
@@ -0,0 +1,233 @@
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