angiosperm_phylogeny	angiosperm_phylogeny
annotation	annotation
binarize_and_transpose	binarize_and_transpose
blast_list	blast_list
check_input	check_input
clusters	clusters
cluster_network	cluster_network
diamond_is_installed	diamond_is_installed
edges	edges
fasta2AAStringSetlist	fasta2AAStringSetlist
find_GS_clusters	find_GS_clusters
gff2GRangesList	gff2GRangesList
infer_microsynteny_phylogeny	infer_microsynteny_phylogeny
infer_syntenet	infer_syntenet
interspecies_synteny	interspecies_synteny
intraspecies_synteny	intraspecies_synteny
iqtree_is_installed	iqtree_is_installed
network	network
parse_collinearity	parse_collinearity
phylogenomic_profile	phylogenomic_profile
plot_network	plot_network
plot_profiles	plot_profiles
process_input	process_input
profiles2phylip	profiles2phylip
proteomes	proteomes
rcpp_mcscanx_file	rcpp_mcscanx_file
run_diamond	run_diamond
