ClstrArc-class          Cluster record archive
ClstrRec-class          Cluster record
Phylota-class           Phylota object
SeqArc-class            Sequence record archive
SeqRec-class            Sequence record
TaxDict-class           Taxonomic record dictionary
TaxRec-class            Taxonomic record
aotus                   Example phylota object (aotus)
batcher                 Download in batches
blast_clstr             Cluster BLAST Results
blast_filter            Filter BLAST results
blast_setup             Ensures NCBI BLAST tools are installed
blast_sqs               BLAST All vs All
blastcache_load         Load BLAST results from cache
blastcache_save         Save BLAST results to cache
blastdb_gen             Generate a BLAST database
blastn_run              Launch blastn
bromeliads              Example phylota object (bromeliads)
cache_rm                Delete a cache
cache_setup             Set-up a cache
calc_mad                Calculate MAD score
calc_wrdfrq             Calculate word frequencies
clade_select            Get all node IDs that will be processed
clstr2_calc             Cluster sets of clusters identified in cluster
                        stage
clstr_all               Hierarchically cluster all sequences of a txid
clstr_direct            Cluster sequences directly associated with txid
clstr_sqs               Identify clusters from sequences
clstr_subtree           Cluster all sequences descending from a txid
clstrarc_gen            Generate cluster archive container class
clstrarc_join           Join two cluster archive
clstrrec_gen            Generate list of clusters
clstrs_calc             Calculate clusters for all sequences in wd
clstrs_join             Join clusters for merging
clstrs_merge            Merge joined clusters
clstrs_renumber         Renumber cluster IDs
clstrs_save             Save clusters to cache
clusters2_run           Run the cluster2 stage
clusters_run            Run the cluster stage
cmdln                   Run a command via terminal/command prompt
cycads                  Example phylota object (cycads)
descendants_get         Get descendants
download_obj_check      Check an object returned from rentrez function
download_run            Run download stage
dragonflies             Example phylota object (dragonflies)
drop_by_rank            Reduce clusters to specific rank
drop_clstrs             Drop cluster records from phylota object
drop_sqs                Drop sequences in a cluster
error                   Write error message to log
get_clstr_slot          Get slot data for each cluster record
get_nsqs                Count number of sequences
get_ntaxa               Count number of unique taxa
get_sq_slot             Get slot data for each sequence
get_stage_times         Get run times for different stages
get_tx_slot             Get slot data for each taxon record
get_txids               Get taxonomic IDs by rank
hierarchic_download     Hierarchically get sequences for a txid
info                    Write info message to log
is_txid_in_clstr        Is txid in cluster?
is_txid_in_sq           Is txid in sequence?
list_clstrrec_slots     List all ClstrRec slots
list_ncbi_ranks         List all NCBI Ranks
list_seqrec_slots       List all SeqRec slots
list_taxrec_slots       List all TaxRec slots
mk_txid_in_sq_mtrx      Return matrix of txid in sequence
ncbicache_load          Retrieve cached NCBI query
ncbicache_save          Save NCBI query result to cache
obj_check               Check if an object exists
obj_load                Load a named object from the cache
obj_save                Save a named object in the cache
parameters              Default parameters
parameters_load         Load parameters from cache
parameters_reset        Change parameters in a working directory
parameters_setup        Set Up Parameters
parent_get              Get taxonomic parent
plot_phylota_pa         Plot presence/absence matrix
plot_phylota_treemap    Plot treemap of Phylota object
progress_init           Initialise progress list in cache
progress_read           Read the progress from cache
progress_reset          Reset progress
progress_save           Save current progress
rank_get                Get rank
read_phylota            Generate a Phylota object in R
reset                   Reset a phylotaR pipeline run
restart                 Restart a phylotaR pipeline run
run                     Run phylotaR pipeline
safely_connect          Safely run rentrez function
search_and_cache        Run rentrez function and cache results
searchterm_gen          Construct GenBank Search Term
seeds_blast             BLAST seed sequences
seq_download            Download sequences for txids
seqarc_gen              Generate sequence archive
seqrec_augment          Augment sequence records list
seqrec_convert          Convert raw Entrez gbwithparts record to
                        SeqRecs
seqrec_gen              Generate sequence record
seqrec_get              seqrec_get
setup                   Set-up parameters
sids_check              Check if sids exist
sids_get                Return random set of sequence IDs
sids_load               Load sids from cache
sids_save               Save sids to cache
sqs_count               Count number of sequences for txid
sqs_load                Load sequences from cache
sqs_save                Save sequences to cache
stage_args_check        Check stage arguments
stages_run              Sequentially run each stage
sturgeons               Example phylota object (sturgeons)
summary_phylota         Summarise clusters in Phylota Table
tardigrades             Example phylota object (tardigrades)
tax_download            Download taxonomic records
taxdict_gen             Generate taxonomic dictionary
taxise_run              Run taxise stage
taxtree_gen             Generate taxonomic tree
tinamous                Example phylota object (tinamous)
txids_get               Searches for descendant taxonomic IDs
txnds_count             Count number of descending taxonomic nodes
update_phylota          Update slots
warn                    Write warning message to log
write_sqs               Write out sequences
yeasts                  Example phylota object (yeasts)
