.acquire_log_lock	dot-acquire_log_lock
.rclade_extract_config	dot-rclade_extract_config
.release_log_lock	dot-release_log_lock
add_clip_off	add_clip_off
add_geo_events	add_geo_events
add_geo_timescale	add_geo_timescale
add_hpd_range	add_hpd_range
add_smart_legend	add_smart_legend
add_support_labels	add_support_labels
annotate_clade	annotate_clade
batch_plot	batch_plot
batch_with_interrupt	batch_with_interrupt
build_base_tree	build_base_tree
build_full_taxa_df	build_full_taxa_df
build_group_vec	build_group_vec
build_path	build_path
build_plot_timetree_params	build_plot_timetree_params
build_taxonomy_lookup	build_taxonomy_lookup
check_dependency	check_dependency
check_example_tree	check_example_tree
check_input_validation	check_input_validation
check_malicious_chars	check_malicious_chars
check_monophyly	check_monophyly
check_monophyly_logic	check_monophyly_logic
check_special_monophyly	check_special_monophyly
check_taxonomy_extraction	check_taxonomy_extraction
cleanup_on_interrupt	cleanup_on_interrupt
compute_legend_layout	compute_legend_layout
compute_mrca_map	compute_mrca_map
compute_time_breaks	compute_time_breaks
compute_x_min	compute_x_min
convert_unit	convert_unit
detect_alphabet	detect_alphabet
detect_encoding	detect_encoding
detect_sequence_format	detect_sequence_format
detect_taxonomy_format	detect_taxonomy_format
detect_tree_format	detect_tree_format
ensure_dir	ensure_dir
escape_regex	escape_regex
example_tree	example_tree
find_rank_cycles	find_rank_cycles
format_elapsed	format_elapsed
format_step	format_step
format_timestamp	format_timestamp
generate_colors	generate_colors
get_dependency_versions	get_dependency_versions
get_git_hash	get_git_hash
get_level_prefix	get_level_prefix
get_progress_summary	get_progress_summary
get_rank_name	get_rank_name
get_supported_extensions	get_supported_extensions
get_taxonomy_levels	get_taxonomy_levels
get_version_string	get_version_string
highlight_clades	highlight_clades
init_progress_tracking	init_progress_tracking
init_steps	init_steps
level_to_num	level_to_num
log_critical	log_critical
log_debug	log_debug
log_error	log_error
log_info	log_info
log_keyvalue	log_keyvalue
log_memory	log_memory
log_message	log_message
log_progress	log_progress
log_section	log_section
log_stats	log_stats
log_subsection	log_subsection
log_table	log_table
log_warning	log_warning
managed_tempdir	managed_tempdir
managed_tempfile	managed_tempfile
next_step	next_step
normalize_file_newlines	normalize_file_newlines
normalize_newlines	normalize_newlines
normalize_rank	normalize_rank
parse_custom_rank	parse_custom_rank
parse_custom_regex	parse_custom_regex
parse_embedded	parse_embedded
parse_gtdb	parse_gtdb
parse_ncbi	parse_ncbi
parse_plot_params	parse_plot_params
parse_semicolon_delimited	parse_semicolon_delimited
parse_silva	parse_silva
parse_taxonomy	parse_taxonomy
parse_taxonomy_with_file	parse_taxonomy_with_file
plot_timetree	plot_timetree
polytomy_tree	polytomy_tree
prepare_geo_timescales	prepare_geo_timescales
print.rclade_options	print.rclade_options
print_version	print_version
pt_single_tree	pt_single_tree
pt_step1_prepare_inputs	pt_step1_prepare_inputs
pt_step2_resolve_taxonomy	pt_step2_resolve_taxonomy
pt_step3_compute_mrca	pt_step3_compute_mrca
pt_step4_generate_colors	pt_step4_generate_colors
pt_step5_render_and_collapse	pt_step5_render_and_collapse
pt_step6_add_annotations	pt_step6_add_annotations
pt_step7_finalize_plot	pt_step7_finalize_plot
RCLADE_HADEAN_END	RCLADE_HADEAN_END
rclade_logger	rclade_logger
rclade_logo	rclade_logo
rclade_options	rclade_options
RCLADE_X_MARGIN_FACTOR	RCLADE_X_MARGIN_FACTOR
RCLADE_X_MIN_FLOOR	RCLADE_X_MIN_FLOOR
read_file_utf8	read_file_utf8
read_taxonomy_file	read_taxonomy_file
read_tree_auto	read_tree_auto
resolve_group	resolve_group
resolve_special_identifier	resolve_special_identifier
resolve_target_domains	resolve_target_domains
resolve_taxonomy_source_priority	resolve_taxonomy_source_priority
run_rclade_cli	run_rclade_cli
run_rclade_selftest	run_rclade_selftest
run_rclade_shiny	run_rclade_shiny
save_session_info	save_session_info
save_timetree	save_timetree
selftest_report	selftest_report
set_log_enabled	set_log_enabled
set_log_file	set_log_file
set_log_level	set_log_level
sort_by_depth	sort_by_depth
split_legend	split_legend
strip_tree_annotations	strip_tree_annotations
summarize_multi_trees	summarize_multi_trees
summarize_taxonomy_quality	summarize_taxonomy_quality
summarize_taxonomy_quality_with_file	summarize_taxonomy_quality_with_file
summarize_timetree	summarize_timetree
SUPPORTED_TREE_EXTENSIONS	SUPPORTED_TREE_EXTENSIONS
theme_timetree	theme_timetree
timer_start	timer_start
timer_stop	timer_stop
update_progress	update_progress
validate_cli_params	validate_cli_params
validate_collapse_plan	validate_collapse_plan
validate_custom_groups	validate_custom_groups
validate_fasta_content	validate_fasta_content
validate_fastq_content	validate_fastq_content
validate_file_exists	validate_file_exists
validate_file_not_empty	validate_file_not_empty
validate_inputs	validate_inputs
validate_newick_syntax	validate_newick_syntax
validate_sequence_deep	validate_sequence_deep
validate_sequence_file	validate_sequence_file
validate_taxonomy_no_cycles	validate_taxonomy_no_cycles
validate_tree_deep	validate_tree_deep
validate_tree_sequence_match	validate_tree_sequence_match
validate_tree_structure	validate_tree_structure
with_graceful_interrupt	with_graceful_interrupt
write_file_utf8	write_file_utf8
