<commit_before>{
  "categories": {
    "Sequence similarity search": {
      "Statistics": [
        "BedGraph.tad.rb",
        "BlastPairwise.AAsubs.pl",
        "BlastTab.advance.bash",
        "BlastTab.recplot2.R",
        "BlastTab.seqdepth.pl",
        "BlastTab.seqdepth_nomedian.pl",
        "BlastTab.seqdepth_ZIP.pl",
        "BlastTab.sumPerHit.pl",
        "FastQ.test-error.rb",
        "RecPlot2.compareIdentities.R"
      ],
      "Manipulation": [
        "BlastTab.addlen.rb",
        "BlastTab.best_hit_sorted.pl",
        "BlastTab.catsbj.pl",
        "BlastTab.cogCat.rb",
        "BlastTab.filter.pl",
        "BlastTab.kegg_pep2path_rest.pl",
        "BlastTab.pairedHits.rb",
        "BlastTab.subsample.pl",
        "BlastTab.taxid2taxrank.pl",
        "BlastTab.topHits_sorted.rb"
      ],
      "Execution": [
        "aai.rb",
        "ani.rb",
        "rbm.rb"
      ]
    },
    "Sequence analyses": {
      "Statistics": [
        "FastA.gc.pl",
        "FastA.length.pl",
        "FastA.N50.pl",
        "FastA.qlen.pl",
        "FastQ.test-error.rb"
      ],
      "Manipulation": [
        "FastA.filter.pl",
        "FastA.filterLen.pl",
        "FastA.filterN.pl",
        "FastA.fragment.rb",
        "FastA.interpose.pl",
        "FastA.per_file.pl",
        "FastA.rename.pl",
        "FastA.revcom.pl",
        "FastA.slider.pl",
        "FastA.split.pl",
        "FastA.split.rb",
        "FastA.subsample.pl",
        "FastA.tag.rb",
        "FastA.wrap.rb",
        "FastQ.filter.pl",
        "FastQ.interpose.pl",
        "FastQ.offset.pl",
        "FastQ.split.pl",
        "FastQ.tag.rb",
        "FastQ.toFastA.awk"
      ]
    },
    "Diversity": {
      "Community": [
        "AlphaDiversity.pl",
        "Chao1.pl",
        "Table.barplot.R"
      ],
      "Population": [
        "VCF.SNPs.rb",
        "VCF.KaKs.rb"
      ]
    },
    "Annotation": {
      "Database mapping": [
        "BlastTab.kegg_pep2path_rest.pl",
        "BlastTab.taxid2taxrank.pl",
        "EBIseq2tax.rb",
        "NCBIacc2tax.rb",
        "gi2tax.rb",
        "M5nr.getSequences.rb",
        "RefSeq.download.bash",
        "SRA.download.bash"
      ],
      "Tables": [
        "Table.barplot.R",
        "GenBank.add_fields.rb",
        "MyTaxa.fragsByTax.pl",
        "Table.df2dist.R",
        "Table.filter.pl",
        "Table.merge.pl",
        "Table.replace.rb",
        "Table.round.rb",
        "Table.split.pl"
      ],
      "Search": [
        "HMM.essential.rb",
        "HMMsearch.extractIds.rb",
        "ogs.annotate.rb",
        "ogs.core-pan.rb",
        "ogs.extract.rb",
        "ogs.mcl.rb",
        "ogs.stats.rb",
        "ogs.rb"
      ]
    },
    "Other data": {
      "Phylogenetic and other distances": [
        "CharTable.classify.rb",
        "JPlace.distances.rb",
        "JPlace.to_iToL.rb",
        "Newick.autoprune.R",
        "TRIBS.test.R",
        "TRIBS.plot-test.R",
        "Table.df2dist.R"
      ],
      "Taxonomic": [
        "CharTable.classify.rb",
        "EBIseq2tax.rb",
        "NCBIacc2tax.rb",
        "Table.barplot.R",
        "gi2tax.rb",
        "MyTaxa.fragsByTax.pl",
        "MyTaxa.seq-taxrank.rb",
        "Taxonomy.silva2ncbi.rb"
      ],
      "Alignments": [
        "AAsubs.log2ratio.rb",
        "Aln.cat.rb",
        "Aln.convert.pl",
        "BlastPairwise.AAsubs.pl"
      ],
      "Clustering": [
        "ogs.mcl.rb",
        "clust.rand.rb"
      ],
      "Read recruitments": [
        "BedGraph.tad.rb",
        "BlastTab.pairedHits.rb",
        "BlastTab.recplot2.R",<commit_msg>BlastTab.catsbj.pl -> Read recruitments subcategory<commit_after>{
  "categories": {
    "Sequence similarity search": {
      "Statistics": [
        "BedGraph.tad.rb",
        "BlastPairwise.AAsubs.pl",
        "BlastTab.advance.bash",
        "BlastTab.recplot2.R",
        "BlastTab.seqdepth.pl",
        "BlastTab.seqdepth_nomedian.pl",
        "BlastTab.seqdepth_ZIP.pl",
        "BlastTab.sumPerHit.pl",
        "FastQ.test-error.rb",
        "RecPlot2.compareIdentities.R"
      ],
      "Manipulation": [
        "BlastTab.addlen.rb",
        "BlastTab.best_hit_sorted.pl",
        "BlastTab.catsbj.pl",
        "BlastTab.cogCat.rb",
        "BlastTab.filter.pl",
        "BlastTab.kegg_pep2path_rest.pl",
        "BlastTab.pairedHits.rb",
        "BlastTab.subsample.pl",
        "BlastTab.taxid2taxrank.pl",
        "BlastTab.topHits_sorted.rb"
      ],
      "Execution": [
        "aai.rb",
        "ani.rb",
        "rbm.rb"
      ]
    },
    "Sequence analyses": {
      "Statistics": [
        "FastA.gc.pl",
        "FastA.length.pl",
        "FastA.N50.pl",
        "FastA.qlen.pl",
        "FastQ.test-error.rb"
      ],
      "Manipulation": [
        "FastA.filter.pl",
        "FastA.filterLen.pl",
        "FastA.filterN.pl",
        "FastA.fragment.rb",
        "FastA.interpose.pl",
        "FastA.per_file.pl",
        "FastA.rename.pl",
        "FastA.revcom.pl",
        "FastA.slider.pl",
        "FastA.split.pl",
        "FastA.split.rb",
        "FastA.subsample.pl",
        "FastA.tag.rb",
        "FastA.wrap.rb",
        "FastQ.filter.pl",
        "FastQ.interpose.pl",
        "FastQ.offset.pl",
        "FastQ.split.pl",
        "FastQ.tag.rb",
        "FastQ.toFastA.awk"
      ]
    },
    "Diversity": {
      "Community": [
        "AlphaDiversity.pl",
        "Chao1.pl",
        "Table.barplot.R"
      ],
      "Population": [
        "VCF.SNPs.rb",
        "VCF.KaKs.rb"
      ]
    },
    "Annotation": {
      "Database mapping": [
        "BlastTab.kegg_pep2path_rest.pl",
        "BlastTab.taxid2taxrank.pl",
        "EBIseq2tax.rb",
        "NCBIacc2tax.rb",
        "gi2tax.rb",
        "M5nr.getSequences.rb",
        "RefSeq.download.bash",
        "SRA.download.bash"
      ],
      "Tables": [
        "Table.barplot.R",
        "GenBank.add_fields.rb",
        "MyTaxa.fragsByTax.pl",
        "Table.df2dist.R",
        "Table.filter.pl",
        "Table.merge.pl",
        "Table.replace.rb",
        "Table.round.rb",
        "Table.split.pl"
      ],
      "Search": [
        "HMM.essential.rb",
        "HMMsearch.extractIds.rb",
        "ogs.annotate.rb",
        "ogs.core-pan.rb",
        "ogs.extract.rb",
        "ogs.mcl.rb",
        "ogs.stats.rb",
        "ogs.rb"
      ]
    },
    "Other data": {
      "Phylogenetic and other distances": [
        "CharTable.classify.rb",
        "JPlace.distances.rb",
        "JPlace.to_iToL.rb",
        "Newick.autoprune.R",
        "TRIBS.test.R",
        "TRIBS.plot-test.R",
        "Table.df2dist.R"
      ],
      "Taxonomic": [
        "CharTable.classify.rb",
        "EBIseq2tax.rb",
        "NCBIacc2tax.rb",
        "Table.barplot.R",
        "gi2tax.rb",
        "MyTaxa.fragsByTax.pl",
        "MyTaxa.seq-taxrank.rb",
        "Taxonomy.silva2ncbi.rb"
      ],
      "Alignments": [
        "AAsubs.log2ratio.rb",
        "Aln.cat.rb",
        "Aln.convert.pl",
        "BlastPairwise.AAsubs.pl"
      ],
      "Clustering": [
        "ogs.mcl.rb",
        "clust.rand.rb"
      ],
      "Read recruitments": [
        "BedGraph.tad.rb",
        "BlastTab.catsbj.pl",
        "BlastTab.pairedHits.rb",
        "BlastTab.recplot2.R",
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