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Results

TSVs

  • buckley_sword.tsv - SWORD results from the Buckley database
  • buckley_sword_hits.tsv - top SWORD results from the Buckley database (AlnLength ≥ 220)
  • evalue_taxonomy.tsv - all sequences that meet ≤ e-10 cutoff (very large files, found on Zenodo)
  • filteredhits.tsv - genomes that have all three genes within a group (i.e. nifHDK) from tophits.tsv
  • filteredfasta.tsv - genomes that have all three genes within a group (i.e. nifHDK) from topfasta.tsv
  • fungene_sword.tsv - SWORD results from the FunGene nifH database
  • fungene_sword_hits.tsv - top SWORD results from the FunGene nifH database (AlnLength ≥ 220)
  • mise_sword.tsv - SWORD results from the Mise database
  • mise_sword_hits.tsv - top SWORD results from the Mise database (AlnLength ≥ 220)
  • NFixDB-v2.tsv - all results from iteration 3 compiled together
  • NFixDB_Buckley_hits.tsv - results from running our HMMs on Buckley's nifH database
  • NFixDB_FunGene_hits.tsv - results from running our HMMs on FunGene's nifH, nifD, and vnfD database
  • NFixDB_Mise_hits.tsv - results from running our HMMs on Mise's nifH database
  • NFixDB_Zehr_hits.tsv - results from running our HMMs on Zehr's nifH database
  • oDB_class-97.tsv - results from running our HMMs on all outside databases
  • oDB_hits-97.tsv - filtered results from running our HMMs on all outside databases
  • topfasta.tsv - top results of each gene from evalue_taxonomy.tsv that are within cutoff of ≤ e-15, bitscore of ≥ 50, or alignment length of > 125
  • tophits.tsv - top results of each gene from evalue_taxonomy.tsv. Zipped due to large size
  • zehr_sword.tsv - SWORD results from the Zehr database
  • zehr_sword_hits.tsv - top SWORD results from the Zehrs database (AlnLength ≥ 220)