beastier-package	beastier-package
add_quotes_if_has_spaces	add_quotes_if_has_spaces
are_beast2_input_lines	are_beast2_input_lines
are_beast2_input_lines_deep	are_beast2_input_lines_deep
are_beast2_input_lines_fast	are_beast2_input_lines_fast
are_identical_alignments	are_identical_alignments
beast2_options_to_table	beast2_options_to_table
beastier	beastier-package
beastier_report	beastier_report
check_beast2	check_beast2
check_beast2_options	check_beast2_options
check_beast2_optionses	check_beast2_optionses
check_beast2_options_data_types	check_beast2_options_data_types
check_beast2_options_do_not_overwrite_existing_files	check_beast2_options_do_not_overwrite_existing_files
check_beast2_options_filenames_differ	check_beast2_options_filenames_differ
check_beast2_options_names	check_beast2_options_names
check_beast2_path	check_beast2_path
check_can_create_dir_for_state_output_file	check_can_create_dir_for_state_output_file
check_can_create_file	check_can_create_file
check_can_create_screenlog_file	check_can_create_screenlog_file
check_can_create_state_output_file	check_can_create_state_output_file
check_can_create_tracelog_file	check_can_create_tracelog_file
check_can_create_treelog_file	check_can_create_treelog_file
check_empty_beastier_folder	check_empty_beastier_folder
check_empty_beaustier_folders	check_empty_beaustier_folders
check_input_filename	check_input_filename
check_input_filename_validity	check_input_filename_validity
check_n_threads	check_n_threads
check_os	check_os
check_rng_seed	check_rng_seed
continue_beast2	continue_beast2
create_beast2_continue_cmd_from_options	create_beast2_continue_cmd_from_options
create_beast2_input_file_folder	create_beast2_input_file_folder
create_beast2_options	create_beast2_options
create_beast2_run_cmd	create_beast2_run_cmd
create_beast2_run_cmd_from_options	create_beast2_run_cmd_from_options
create_beast2_screenlog_folder	create_beast2_screenlog_folder
create_beast2_state_output_file_folder	create_beast2_state_output_file_folder
create_beast2_tracelog_folder	create_beast2_tracelog_folder
create_beast2_treelog_folder	create_beast2_treelog_folder
create_beast2_validate_cmd	create_beast2_validate_cmd
create_beast2_validate_cmd_bin	create_beast2_validate_cmd_bin
create_beast2_validate_cmd_jar	create_beast2_validate_cmd_jar
create_beast2_version_cmd	create_beast2_version_cmd
create_beast2_version_cmd_bin	create_beast2_version_cmd_bin
create_beast2_version_cmd_jar	create_beast2_version_cmd_jar
create_beastier_tempfolder	create_beastier_tempfolder
create_mcbette_beast2_options	create_mcbette_beast2_options
create_random_alignment	create_random_alignment
create_random_fasta	create_random_fasta
create_random_phylogeny	create_random_phylogeny
create_temp_input_filename	create_temp_input_filename
create_temp_state_filename	create_temp_state_filename
default_params_doc	default_params_doc
do_minimal_run	do_minimal_run
extract_screenlog_filename_from_beast2_input_file	extract_screenlog_filename_from_beast2_input_file
extract_tracelog_filename_from_beast2_input_file	extract_tracelog_filename_from_beast2_input_file
extract_treelog_filename_from_beast2_input_file	extract_treelog_filename_from_beast2_input_file
get_alignment_ids_from_xml_filename	get_alignment_ids_from_xml_filename
get_beast2_example_filename	get_beast2_example_filename
get_beast2_example_filenames	get_beast2_example_filenames
get_beast2_main_class_name	get_beast2_main_class_name
get_beast2_options_filenames	get_beast2_options_filenames
get_beast2_version	get_beast2_version
get_beastier_folder	get_beastier_folder
get_beastier_path	get_beastier_path
get_beastier_paths	get_beastier_paths
get_beastier_tempfilename	get_beastier_tempfilename
get_default_beast2_bin_path	get_default_beast2_bin_path
get_default_beast2_download_url	get_default_beast2_download_url
get_default_beast2_download_url_linux	get_default_beast2_download_url_linux
get_default_beast2_download_url_win	get_default_beast2_download_url_win
get_default_beast2_folder	get_default_beast2_folder
get_default_beast2_jar_path	get_default_beast2_jar_path
get_default_beast2_path	get_default_beast2_path
get_default_beast2_version	get_default_beast2_version
get_default_java_path	get_default_java_path
get_duplicate_param_ids	get_duplicate_param_ids
get_java_version	get_java_version
get_trees_filenames	get_trees_filenames
gives_beast2_warning	gives_beast2_warning
has_unique_ids	has_unique_ids
install_beast2	install_beast2
is_alignment	is_alignment
is_beast2_input_file	is_beast2_input_file
is_beast2_installed	is_beast2_installed
is_bin_path	is_bin_path
is_jar_path	is_jar_path
is_on_appveyor	is_on_appveyor
is_on_ci	is_on_ci
is_on_travis	is_on_travis
is_win_bin_path	is_win_bin_path
print_beast2_options	print_beast2_options
remove_beastier_folder	remove_beastier_folder
remove_beaustier_folders	remove_beaustier_folders
remove_file_if_present	remove_file_if_present
rename_beast2_options_filenames	rename_beast2_options_filenames
run_beast2	run_beast2
run_beast2_from_options	run_beast2_from_options
save_lines	save_lines
save_nexus_as_fasta	save_nexus_as_fasta
uninstall_beast2	uninstall_beast2
upgrade_beast2	upgrade_beast2
