Prepare Custom Database

  1. Retrieve the recommended PhyloFisher directory structure, OrthoMCL database, example metadata.tsv, and tree_colors.tsv file via wget
    wget https://ndownloader.figshare.com/files/29093325
  2. Uncompress the file 29093325
    tar -xzvf 29093325
  3. Move into the directory PhyloFisher_FOR_CUSTOM_DATABASE
    cd PhyloFisher_FOR_CUSTOM_DATABASE
  4. Place your single gene files of orthologs in the directory /database/orthologs/
    • The ortholog files must be in fasta format.
    • Each ortholog file must be named with the following convention {gene_name}.fas.
      • Ex. RPL7.fas
    • Each individual taxon should have a Unique ID as the header in all ortholog files. This Unique ID must be the the same in all ortholog files.
    • Each taxon can be present only once in each ortholog file.
  5. Place files of known paralogs for each gene in the directory /database/paralogs/ (OPTIONAL)
    • Each gene file must be named with the following convention {gene_name}_paralogs.fas.
      • Ex. RPL7_paralogs.fas
    • Each individual taxon should have a Unique ID as the header in all paralog files. This Unique ID must be the the same in all paralog files and the corresponding ortholog files.
    • Each taxon can be present more than once in each paralog file.
  6. Place the complete proteome of each taxon present in the ortholog files in /database/proteomes
    • All proteomes must be in fasta format
    • All proteomes must be tar and gzipped and follow the naming convention {Unique ID}.tar.gz

  7. Fill out the metadata.tsv file found in PhyloFisher_FOR_CUSTOM_DATABASE/database </br> Detailed instructions on preparing the metadata.tsv file can be found here.

  8. Run build_database.py. Detailed instructions on build_database.py can be found here.

Some notes about sequence headers:

  • Each sequence header (sequence header = Unique ID) within a file must be unique. Sequence headers must be the same across all files for a taxon and must be the same as the Unique ID provided in the metadata.tsv file for the taxon. This is true for both ortholog and paralog fasta files.
  • Sequence headers cannot contain underscores “_”, at symbols “@”, white spaces, or double dots “..”. This is true for both ortholog and paralog fasta files.
  • If you provided separate sequence files containing paralogs, each sequence header within each file will have “..p” appended to the end by `build_database.py`.