Article - MPS-Sampling

All the data about the article of MPS-Sampling.

• MPS-Samping (data of the analysis from MPS-Sampling)
• • ADB (Artificial genomes generated from RiboDB data)
  • • data
    • • fasta.tar.gz (a file to unzip, containing all the protein sequences from GTDB)
      • genome_index (the index csv file used by MPS-Sampling)
    • Samples
    • • Sample_X (a directory for each tested sample)
      • • input
        • • genome_index (the index csv file used by MPS-Sampling)
        • output
        • • 4.MPS_results_directory
          • • e_value_1e-05_cov_mode_0_min_cov_0.8_min_seq_id_0.6
            • • delta_0.4
              • • MPS_links.csv (A file with two columns, containing the link between each original genome (first column) and its MPS-representative (second column).)
                • MPS_representatives.csv (A file with one column, contain the MPS-representatives chosen by MPS-Sampling.)
  • GTDB (Genome-Based Database)
  • • input
    • • fasta.tar.gz (a file to unzip, containing all the protein sequences from GTDB)
      • genome_index.csv (the index csv file used by MPS-Sampling)
    • output
    • • 4.MPS_results_directory
      • • e_value_1e-05_cov_mode_0_min_cov_0.8_min_seq_id_0.6
        • • delta_X (There is a directory for each delta from {0.05, 0.1, ... , 0.95, 1}.)
          • • MPS_links.csv (A file with two columns, containing the link between each original genome (first column) and its MPS-representative (second column).)
            • MPS_representatives.csv (A file with one column, contain the MPS-representatives chosen by MPS-Sampling.)
  • RiboDB (Ribosomal Database)
  • • input
    • • fasta.tar.gz (a file to unzip, containing all the protein sequences from RiboDB, after filtering)
      • genome_index.csv (the index csv file used by MPS-Sampling)
    • output
    • • 4.MPS_results_directory
      • • e_value_1e-05_cov_mode_0_min_cov_0.8_min_seq_id_0.6
        • • delta_X (There is a directory for each delta from {0.05, 0.1, ... , 0.95, 1}.)
          • • MPS_links.csv (A file with two columns, containing the link between each original genome (first column) and its MPS-representative (second column).)
            • MPS_representatives.csv (A file with one column, contain the MPS-representatives chosen by MPS-Sampling.)
• phylogeny (data about the phylogenetic inference)
• • Bacillaceae
  • • concat_cleaned.fst (the supermatrix used for the phylogenetic inference)
    • FastTree_iTOL.nw (the inferred phylogeny, as it was used on iTOL)
  • Bacterial backbone
  • • concat_cleaned.fst (the supermatrix used for the phylogenetic inference)
    • FastTree_iTOL.nw (the inferred phylogeny, as it was used on iTOL)
  • Enterobacteriaceae
  • • concat_cleaned.fst (the supermatrix used for the phylogenetic inference)
    • FastTree_iTOL.nw (the inferred phylogeny, as it was used on iTOL)
  • Lactobacillaceae
  • • concat_cleaned.fst (the supermatrix used for the phylogenetic inference)
    • FastTree_iTOL.nw (the inferred phylogeny, as it was used on iTOL)