API for beastier
Call 'BEAST2'

Global functions
add_quotes_if_has_spaces Man page Source code
are_beast2_input_lines Man page Source code
are_beast2_input_lines_deep Man page Source code
are_beast2_input_lines_fast Man page Source code
are_identical_alignments Man page Source code
beast2_options_to_table Man page Source code
beastier Man page
beastier_report Man page Source code
check_beast2 Man page Source code
check_beast2_options Man page Source code
check_beast2_options_data_types Man page Source code
check_beast2_options_do_not_overwrite_existing_files Man page Source code
check_beast2_options_filenames_differ Man page Source code
check_beast2_options_names Man page Source code
check_beast2_optionses Man page Source code
check_beast2_path Man page Source code
check_can_create_dir_for_state_output_file Man page Source code
check_can_create_file Man page Source code
check_can_create_screenlog_file Man page Source code
check_can_create_state_output_file Man page Source code
check_can_create_tracelog_file Man page Source code
check_can_create_treelog_file Man page Source code
check_empty_beastier_folder Man page Source code
check_input_filename Man page Source code
check_input_filename_validity Man page Source code
check_n_threads Man page Source code
check_os Man page Source code
check_rng_seed Man page Source code
continue_beast2 Man page Source code
create_beast2_continue_cmd_from_options Man page Source code
create_beast2_input_file_folder Man page Source code
create_beast2_options Man page Source code
create_beast2_run_cmd Man page Source code
create_beast2_run_cmd_from_options Man page Source code
create_beast2_screenlog_folder Man page Source code
create_beast2_state_output_file_folder Man page Source code
create_beast2_tracelog_folder Man page Source code
create_beast2_treelog_folder Man page Source code
create_beast2_validate_cmd Man page Source code
create_beast2_validate_cmd_bin Man page Source code
create_beast2_validate_cmd_jar Man page Source code
create_beast2_version_cmd Man page Source code
create_beast2_version_cmd_bin Man page Source code
create_beast2_version_cmd_jar Man page Source code
create_beastier_tempfolder Man page Source code
create_beautier_tempfolder Man page Source code
create_mcbette_beast2_options Man page Source code
create_random_alignment Man page Source code
create_random_fasta Man page Source code
create_random_phylogeny Man page Source code
create_temp_input_filename Man page Source code
create_temp_state_filename Man page Source code
default_params_doc Man page Source code
do_minimal_run Man page Source code
extract_screenlog_filename_from_beast2_input_file Man page Source code
extract_tracelog_filename_from_beast2_input_file Man page Source code
extract_treelog_filename_from_beast2_input_file Man page Source code
get_alignment_ids_from_xml_filename Man page Source code
get_beast2_example_filename Man page Source code
get_beast2_example_filenames Man page Source code
get_beast2_main_class_name Man page Source code
get_beast2_options_filenames Man page Source code
get_beast2_version Man page Source code
get_beastier_folder Man page Source code
get_beastier_path Man page Source code
get_beastier_paths Man page Source code
get_beastier_tempfilename Man page Source code
get_default_beast2_bin_path Man page Source code
get_default_beast2_download_url Man page Source code
get_default_beast2_download_url_linux Man page Source code
get_default_beast2_download_url_win Man page Source code
get_default_beast2_folder Man page Source code
get_default_beast2_jar_path Man page Source code
get_default_beast2_path Man page Source code
get_default_beast2_version Man page Source code
get_default_java_path Man page Source code
get_duplicate_param_ids Man page Source code
get_java_version Man page Source code
get_trees_filenames Man page Source code
gives_beast2_warning Man page Source code
has_unique_ids Man page Source code
install_beast2 Man page Source code
is_alignment Man page Source code
is_beast2_input_file Man page Source code
is_beast2_installed Man page Source code
is_bin_path Man page Source code
is_jar_path Man page Source code
is_on_appveyor Man page Source code
is_on_ci Man page Source code
is_on_travis Man page Source code
is_win_bin_path Man page Source code
print_beast2_options Man page Source code
remove_file_if_present Man page Source code
rename_beast2_options_filenames Man page Source code
run_beast2 Man page Source code
run_beast2_from_options Man page Source code
save_lines Man page Source code
save_nexus_as_fasta Man page Source code
uninstall_beast2 Man page Source code
upgrade_beast2 Man page Source code
beastier documentation built on Sept. 19, 2021, 5:06 p.m.