Download Provided Database

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.