Download Provided Dataset

Download PhyloFisher’s Provided Database

  1. Retrieve the provided starting database via wget:
    wget https://ndownloader.figshare.com/files/29093409
  2. Uncompress the .tar.gz file:
    tar -xzvf 29093409

The uncompressed database directory contains the subdirectories and files detailed below.

  • database/
    • backups/
      • {Month}_{Day}_{Year}.tar.gz a compressed file containing backups of the two database folders orthologs/, paralogs/, the database file metadata.tsv, and tree_colors.tsv
    • datasetdb/
      • datasetdb.dmnd a diamond database of the orthologs
      • datasetdb.fasta a fasta file of the orthologs used to construct the diamond database
    • orthologs/
      • {gene_name}.fas 240 fasta files of the orthologs
    • orthomcl/
      • bacterial abbreviated names of bacterial species present in OrthoMCL
      • gene_og a tsv file detailing the names of the 240 genes and their corresponding OrthoMCL orthogroup number(s)
      • orthomcl.diamonddb.dmnd diamond database of OrthoMCL
    • paralogs/
      • {gene_name}_paralogs.fas 240 fasta files of the paralogs
    • profiles
      • {gene_name}.hmm 240 profile hmm files of the orthologs
    • proteomes/
      • {Unique_ID}.faa.tar.gz complete proteomes of all taxa in the database
    • metadata.tsv tsv file of containing metadata for species in the database. Detailed extensively in the section “Detailed Explanation of the PhyloFisherDatabase_v1.0 Metadata File” of this manual
    • tree_colors.tsv a comma separated file used to color taxa based on taxonomy for manual inspection of single gene trees.