Quickstart

1. Make a project directory (named anything) and move into it
   mkdir <project_directory>
cd <project_directory>

2. explore_database.py
   • Explore the contents of PhyloFisher’s provided starting database (found here: https://ndownloader.figshare.com/files/29093409) to help make decisions on proteomes to add (Optional)
   • Usage: explore_database.py [OPTIONS]
3. Fill out input_metadata.tsv
   • Each proteome to be added to the database should be included
   • See Table 1 for an example and detailed explanation of input_metadata.tsv
4. config.py
   • config.py allows users to configure the analysis directory
   • Usage: config.py [OPTIONS] -d <database_folder> -i <input_file.tsv>
5. fisher.py
   • Run fisher.py for homolog collection.
   • Usage: fisher.py [OPTIONS]
6. informant.py
   • Prepare preliminary statistics for and select organisms and genes prior to homolog tree construction
   • Usage: informant.py [OPTIONS] -i <fisher_out_dir>
     
7. working_dataset_constructor.py
   • Apply your selections from the previous step
   • Usage: working_dataset_constructor.py [OPTIONS] -i <fisher_out_dir>
8. sgt_constructor.py
   • Length filtration, trimming, and homolog tree construction
   • Usage: sgt_constructor.py [OPTIONS] -i <working_dataset_constructor_out_dir>
9. forest.py
   • Tree visualization.
   • Usage: forest.py [OPTIONS] -i <dir_containing_tress>
10. apply_to_db.py
    • Apply parsing decisions and add new data to the database:
    • Usage: apply_to_db.py [OPTIONS] -i <forest_out_dir>
11. select_taxa.py (OPTIONAL)
    • Select a subset of taxa from the database for final phylogenomic analyses.
    • Usage: select_taxa.py [OPTIONS]
12. select_orthologs.py (OPTIONAL)
    • Select a subset of orthologs from the database for final phylogenomic analyses.
    • Usage: select_orthologs.py [OPTIONS]
13. prep_final_dataset.py
    • Collect taxa and genes for final phylogenomic analyses.
    • Usage: prep_final_dataset.py [OPTIONS]
14. matrix_constructor.py
    • Build phylogenomic matrix (Concatenation).
    • Usage: matrix_constructor.py [OPTIONS] -i <prep_final_dataset_out_dir>
      

***Use <script>.py --help to see all options and their descriptions.