SUPFAM
    Domain annotations downloaded from SUPERFAMILY. These were the input to the
    raw data pre-processing module of DomArchov. Each genomic annotation file 
    includes the species identifier and, for each domain, the sequence in which 
    it is found, the first and last amino acid positions for the domain model, 
    and the domain family and superfamily identifiers.

formatted
    DomArchov's raw data pre-processing and precalculation modules take SUPFAM
    annotations and calculate values that are used repeatedly in a typical
    simulation. This directory contains output from these two modules. See lower
    level README for descriptions of the files.

domain_architectures
    Genuine and final simulated (T=3.2M) domain architectures in 4 lineages in
    pkl format. [lineage]_genuine.pkl files are output of DomArchov's
    pre-processing module, extracted directly from SUPFAM annotations.
    [lineage]_simulated.pkl files contain final domain architectures, output by
    the simulator module of DomArchov.

Other folders contain scripts and post-processed data associated with each
individual figure/table.
