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 is ready for further analyses |
clusters | Synteny network clusters of BUSCO genes for 25 eudicot species |
cluster_network | Cluster the synteny network using the Infomap algorithm |
diamond_is_installed | Check if DIAMOND is installed |
edges | Synteny network of Ostreococcus genomes represented as an edge list |
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 |
network | Synteny network of BUSCO genes for 25 eudicot species |
parse_collinearity | Parse .collinearity files into an edge list |
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 |
run_diamond | Wrapper to run DIAMOND from an R session |