# Inference And Analysis Of Synteny Networks

## Documentation for package ‘syntenet’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
clusters | Synteny network clusters of BUSCO genes for 25 eudicot species
cluster_network | Cluster the synteny network using the Infomap algorithm
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