angiosperm_phylogeny    Microsynteny-based angiosperm phylogeny.
annotation              Filtered genome annotation for Ostreococcus sp.
                        species
binarize_and_transpose
                        Binarize and transpose the phylogenomic profile
                        matrix
blast_list              List of data frames containing BLAST-like
                        tabular output
check_input             Check if input objects are ready for further
                        analyses
cluster_network         Cluster the synteny network using the Infomap
                        algorithm
clusters                Synteny network clusters of BUSCO genes for 25
                        eudicot species
collapse_bidirectional_hits
                        Collapse a list of bidirectional DIAMOND hits
collapse_protein_ids    Collapse protein IDs into gene IDs in sequence
                        names of AAStringSet objects
create_species_id_table
                        Create a data frame of species IDs
                        (3-5-character abbreviations)
diamond_is_installed    Check if DIAMOND is installed
edges                   Synteny network of Ostreococcus genomes
                        represented as an edge list
export_sequences        Export processed sequences as FASTA files
fasta2AAStringSetlist   Read FASTA files in a directory as a list of
                        AAStringSet objects
find_GS_clusters        Find group-specific clusters based on
                        user-defined species classification
gff2GRangesList         Read GFF/GTF files in a directory as a
                        GRangesList object
infer_microsynteny_phylogeny
                        Infer microsynteny-based phylogeny with IQTREE
infer_syntenet          Infer synteny network
interspecies_synteny    Detect interspecies synteny
intraspecies_synteny    Detect intraspecies synteny
iqtree_is_installed     Check if IQTREE is installed
iqtree_version          Get IQ-TREE version
last_is_installed       Check if last is installed
make_bidirectional      Create a data frame of bidirectional
                        comparisons from unidirectional comparisons
network                 Synteny network of BUSCO genes for 25 eudicot
                        species
parse_collinearity      Parse .collinearity files obtained with MCScan
phylogenomic_profile    Perform phylogenomic profiling for synteny
                        network clusters
plot_network            Plot network
plot_profiles           Plot a heatmap of phylogenomic profiles
process_input           Process sequence data
profiles2phylip         Save the transposed binary profiles matrix to a
                        file in PHYLIP format
proteomes               Filtered proteomes of Ostreococcus sp. species
rcpp_mcscanx_file       rcpp_mcscanx_file
read_diamond            Read DIAMOND/BLAST tables as a list of data
                        frames
run_diamond             Wrapper to run DIAMOND from an R session
run_last                Wrapper to run last from an R session
scerevisiae_annot       Genome annotation of the yeast species S.
                        cerevisiae
scerevisiae_diamond     Intraspecies DIAMOND output for S. cerevisiae
