aotus	aotus
as.character,ClstrArc-method	ClstrArc-class
as.character,ClstrRec-method	ClstrRec-class
as.character,Phylota-method	Phylota-class
as.character,SeqArc-method	SeqArc-class
as.character,SeqRec-method	SeqRec-class
as.character,TaxDict-method	TaxDict-class
as.character,TaxRec-method	TaxRec-class
batcher	batcher
blastcache_load	blastcache_load
blastcache_save	blastcache_save
blastdb_gen	blastdb_gen
blastn_run	blastn_run
blast_clstr	blast_clstr
blast_filter	blast_filter
blast_setup	blast_setup
blast_sqs	blast_sqs
bromeliads	bromeliads
cache_rm	cache_rm
cache_setup	cache_setup
calc_mad	calc_mad
calc_wrdfrq	calc_wrdfrq
clade_select	clade_select
clstr2_calc	clstr2_calc
ClstrArc-class	ClstrArc-class
ClstrArc-method	ClstrArc-class
clstrarc_gen	clstrarc_gen
clstrarc_join	clstrarc_join
ClstrRec-class	ClstrRec-class
ClstrRec-method	ClstrRec-class
clstrrec_gen	clstrrec_gen
clstrs_calc	clstrs_calc
clstrs_join	clstrs_join
clstrs_merge	clstrs_merge
clstrs_renumber	clstrs_renumber
clstrs_save	clstrs_save
clstr_all	clstr_all
clstr_direct	clstr_direct
clstr_sqs	clstr_sqs
clstr_subtree	clstr_subtree
clusters2_run	clusters2_run
clusters_run	clusters_run
cmdln	cmdln
cycads	cycads
descendants_get	descendants_get
download_obj_check	download_obj_check
download_run	download_run
dragonflies	dragonflies
drop_by_rank	drop_by_rank
drop_clstrs	drop_clstrs
drop_sqs	drop_sqs
error	error
get_clstr_slot	get_clstr_slot
get_nsqs	get_nsqs
get_ntaxa	get_ntaxa
get_sq_slot	get_sq_slot
get_stage_times	get_stage_times
get_txids	get_txids
get_tx_slot	get_tx_slot
hierarchic_download	hierarchic_download
info	info
is_txid_in_clstr	is_txid_in_clstr
is_txid_in_sq	is_txid_in_sq
list_clstrrec_slots	list_clstrrec_slots
list_ncbi_ranks	list_ncbi_ranks
list_seqrec_slots	list_seqrec_slots
list_taxrec_slots	list_taxrec_slots
mk_txid_in_sq_mtrx	mk_txid_in_sq_mtrx
ncbicache_load	ncbicache_load
ncbicache_save	ncbicache_save
obj_check	obj_check
obj_load	obj_load
obj_save	obj_save
parameters	parameters
parameters_load	parameters_load
parameters_reset	parameters_reset
parameters_setup	parameters_setup
parent_get	parent_get
Phylota-class	Phylota-class
Phylota-method	Phylota-class
plot_phylota_pa	plot_phylota_pa
plot_phylota_treemap	plot_phylota_treemap
print,ClstrArc-method	ClstrArc-class
print,ClstrRec-method	ClstrRec-class
print,Phylota-method	Phylota-class
print,SeqArc-method	SeqArc-class
print,SeqRec-method	SeqRec-class
print,TaxDict-method	TaxDict-class
print,TaxRec-method	TaxRec-class
progress_init	progress_init
progress_read	progress_read
progress_reset	progress_reset
progress_save	progress_save
rank_get	rank_get
read_phylota	read_phylota
reset	reset
restart	restart
run	run
safely_connect	safely_connect
searchterm_gen	searchterm_gen
search_and_cache	search_and_cache
seeds_blast	seeds_blast
SeqArc-class	SeqArc-class
SeqArc-method	SeqArc-class
seqarc_gen	seqarc_gen
SeqRec-class	SeqRec-class
SeqRec-method	SeqRec-class
seqrec_augment	seqrec_augment
seqrec_convert	seqrec_convert
seqrec_gen	seqrec_gen
seqrec_get	seqrec_get
seq_download	seq_download
setup	setup
show,ClstrArc-method	ClstrArc-class
show,ClstrRec-method	ClstrRec-class
show,Phylota-method	Phylota-class
show,SeqArc-method	SeqArc-class
show,SeqRec-method	SeqRec-class
show,TaxDict-method	TaxDict-class
show,TaxRec-method	TaxRec-class
sids_check	sids_check
sids_get	sids_get
sids_load	sids_load
sids_save	sids_save
sqs_count	sqs_count
sqs_load	sqs_load
sqs_save	sqs_save
stages_run	stages_run
stage_args_check	stage_args_check
str,ClstrArc-method	ClstrArc-class
str,ClstrRec-method	ClstrRec-class
str,Phylota-method	Phylota-class
str,SeqArc-method	SeqArc-class
str,SeqRec-method	SeqRec-class
str,TaxDict-method	TaxDict-class
str,TaxRec-method	TaxRec-class
sturgeons	sturgeons
summary,ClstrArc-method	ClstrArc-class
summary,ClstrRec-method	ClstrRec-class
summary,Phylota-method	Phylota-class
summary,SeqArc-method	SeqArc-class
summary,SeqRec-method	SeqRec-class
summary,TaxDict-method	TaxDict-class
summary,TaxRec-method	TaxRec-class
summary_phylota	summary_phylota
tardigrades	tardigrades
TaxDict-class	TaxDict-class
TaxDict-method	TaxDict-class
taxdict_gen	taxdict_gen
taxise_run	taxise_run
TaxRec-class	TaxRec-class
TaxRec-method	TaxRec-class
taxtree_gen	taxtree_gen
tax_download	tax_download
tinamous	tinamous
txids_get	txids_get
txnds_count	txnds_count
update_phylota	update_phylota
warn	warn
write_sqs	write_sqs
yeasts	yeasts
[,ClstrArc,character,missing,missing-method	ClstrArc-class
[,SeqArc,character,missing,missing-method	SeqArc-class
[[,ClstrArc,character-method	ClstrArc-class
[[,Phylota,character-method	Phylota-class
[[,SeqArc,character-method	SeqArc-class
