assess_orthogroups      Assess orthogroup inference based on functional
                        annotation
assess_synnet           Assess synteny network based on clustering
                        coefficient and node frequency
assess_synnet_list      Assess list of synteny networks as in
                        'assess_synnet'
batch_summary           BUSCO summary output for batch mode
busco_is_installed      Check if BUSCO is installed
calculate_H             Calculate homogeneity scores for orthogroups
compare_orthogroups     Compare inferred orthogroups to a references
                        set
interpro_ath            Intepro annotation for Arabidopsis thaliana's
                        genes
interpro_bol            Intepro annotation for Brassica oleraceae's
                        genes
list_busco_datasets     List BUSCO data sets
og                      Orthogroups between Arabidopsis thaliana and
                        Brassica oleraceae
plot_busco              Plot BUSCO summary output
plot_duplications       Plot species-specific duplications
plot_genes_in_ogs       Plot percentage of genes in orthogroups for
                        each species
plot_og_overlap         Plot pairwise orthogroup overlap between
                        species
plot_og_sizes           Plot orthogroup sizes per species
plot_orthofinder_stats
                        Plot a panel with a summary of Orthofinder
                        stats
plot_species_specific_ogs
                        Plot number of species-specific orthogroups
plot_species_tree       Plot species tree
read_busco              Read and parse BUSCO's summary report
read_orthofinder_stats
                        Read and parse Orthofinder summary statistics
read_orthogroups        Read and parse orthogroups file created by
                        OrthoFinder
run_busco               Run BUSCO assessment of assembly and annotation
                        quality
synnet                  Synteny network for Brassica oleraceae, B.
                        napus, and B. rapa
tree                    Species tree for model species
