API for richelbilderbeek/beautier
'BEAUti' from R

Global functions
are_clock_models Source code
are_equal_xml_files Source code
are_equal_xml_lines Source code
are_equivalent_xml_files Source code
are_equivalent_xml_lines Man page Source code
are_equivalent_xml_lines_all Man page Source code
are_equivalent_xml_lines_loggers Man page Source code
are_equivalent_xml_lines_operators Man page Source code
are_equivalent_xml_lines_section Man page Source code
are_ids Source code
are_init_clock_models Source code
are_init_mrca_priors Source code
are_init_site_models Source code
are_init_tree_priors Source code
are_initial_phylogenies Source code
are_mrca_align_ids_in_fastas Source code
are_mrca_priors Source code
are_mrca_taxa_names_in_fastas Source code
are_mrca_taxa_non_intersecting Source code
are_rln_clock_models Source code
are_site_models Source code
are_tree_priors Source code
bd_tree_prior_to_xml_prior_distr Man page Source code
beautier Man page
beautier-package Man page
cbs_tree_prior_to_xml_prior_distr Man page Source code
ccp_tree_prior_to_xml_prior_distr Man page Source code
cep_tree_prior_to_xml_prior_distr Man page Source code
check_gamma_site_model Source code
check_site_models Source code
clock_model_to_xml_lh_distr Source code
clock_model_to_xml_operators Source code
clock_model_to_xml_prior_distr Source code
clock_model_to_xml_state Source code
clock_model_to_xml_tracelog Source code
clock_model_to_xml_treelogger Source code
clock_models_to_xml_operators Source code
clock_models_to_xml_prior_distr Source code
clock_models_to_xml_state Source code
clock_models_to_xml_tracelog Source code
compare_lines Source code
count_trailing_spaces Source code
create_alpha_param Man page
create_bd_tree_prior Man page
create_beast2_beast_xml Source code
create_beast2_input Man page Source code
create_beast2_input_1_12 Man page Source code
create_beast2_input_beast Source code
create_beast2_input_data Source code
create_beast2_input_data_sequences Source code
create_beast2_input_distr Source code
create_beast2_input_distr_lh Man page Source code
create_beast2_input_distr_prior Man page Source code
create_beast2_input_file Man page Source code
create_beast2_input_file_1_12 Man page Source code
create_beast2_input_init Source code
create_beast2_input_loggers Source code
create_beast2_input_map Source code
create_beast2_input_operators Source code
create_beast2_input_run Source code
create_beast2_input_screenlog Man page Source code
create_beast2_input_state Source code
create_beast2_input_tracelog Man page Source code
create_beast2_input_treelogs Man page Source code
create_beast2_input_xml Man page Source code
create_beta_distr Man page
create_beta_param Man page
create_cbs_tree_prior Man page
create_ccp_tree_prior Man page
create_cep_tree_prior Man page
create_clock_model Man page Source code
create_clock_model_rln Man page
create_clock_model_strict Man page
create_clock_models Man page Source code
create_clock_rate_param Man page
create_data_xml Source code
create_distr Man page Source code
create_distr_beta Man page
create_distr_exp Man page
create_distr_gamma Man page
create_distr_inv_gamma Man page
create_distr_laplace Man page
create_distr_log_normal Man page
create_distr_normal Man page
create_distr_one_div_x Man page
create_distr_poisson Man page
create_distr_uniform Man page
create_exp_distr Man page
create_gamma_distr Man page
create_gamma_site_model Man page Source code
create_gtr_site_model Man page
create_hky_site_model Man page
create_inv_gamma_distr Man page
create_jc69_site_model Man page
create_kappa_1_param Man page
create_kappa_2_param Man page
create_lambda_param Man page
create_laplace_distr Man page
create_log_normal_distr Man page
create_m_param Man page
create_mcmc Man page Source code
create_mcmc_nested_sampling Man page Source code
create_mean_param Man page
create_misc_options Man page Source code
create_mrca_prior Man page Source code
create_mu_param Man page
create_normal_distr Man page
create_one_div_x_distr Man page
create_param Man page Source code
create_param_alpha Man page
create_param_beta Man page
create_param_clock_rate Man page
create_param_kappa_1 Man page
create_param_kappa_2 Man page
create_param_lambda Man page
create_param_m Man page
create_param_mean Man page
create_param_mu Man page
create_param_rate_ac Man page
create_param_rate_ag Man page
create_param_rate_at Man page
create_param_rate_cg Man page
create_param_rate_ct Man page
create_param_rate_gt Man page
create_param_s Man page
create_param_scale Man page
create_param_sigma Man page
create_poisson_distr Man page
create_rate_ac_param Man page
create_rate_ag_param Man page
create_rate_at_param Man page
create_rate_cg_param Man page
create_rate_ct_param Man page
create_rate_gt_param Man page
create_rln_clock_model Man page
create_s_param Man page
create_scale_param Man page
create_sigma_param Man page
create_site_model Man page Source code
create_site_model_gtr Man page
create_site_model_hky Man page
create_site_model_jc69 Man page
create_site_model_tn93 Man page
create_site_models Man page Source code
create_strict_clock_model Man page
create_tn93_site_model Man page
create_trait_set_string Man page Source code
create_tree_prior Man page Source code
create_tree_prior_bd Man page
create_tree_prior_cbs Man page
create_tree_prior_ccp Man page
create_tree_prior_cep Man page
create_tree_prior_yule Man page
create_tree_priors Man page Source code
create_uniform_distr Man page
create_yule_tree_prior Man page
default_parameters_doc Man page Source code
default_params_doc Man page Source code
distr_to_xml Source code
distr_to_xml_beta Man page Source code
distr_to_xml_exp Man page Source code
distr_to_xml_gamma Man page Source code
distr_to_xml_inv_gamma Man page Source code
distr_to_xml_laplace Man page Source code
distr_to_xml_log_normal Man page Source code
distr_to_xml_normal Man page Source code
distr_to_xml_one_div_x Man page Source code
distr_to_xml_poisson Man page Source code
distr_to_xml_uniform Man page Source code
extract_xml_loggers_from_lines Source code
extract_xml_operators_from_lines Source code
extract_xml_section_from_lines Source code
fasta_file_to_sequences Source code
fasta_to_phylo Man page Source code
fastas_to_phylos Man page Source code
files_exist Source code
find_clock_model Source code
find_first_regex_line Source code
find_first_xml_opening_tag_line Source code
find_last_regex_line Source code
find_last_xml_closing_tag_line Source code
freq_equilibrium_to_xml Source code
gamma_site_model_to_xml_prior_distr Source code
gamma_site_model_to_xml_state Source code
gamma_site_models_to_xml_prior_distr Source code
get_alignment_id Man page Source code
get_alignment_ids Man page Source code
get_beautier_path Man page Source code
get_beautier_paths Man page Source code
get_clock_model_name Source code
get_clock_model_names Source code
get_clock_models_ids Source code
get_distr_n_params Source code
get_distr_names Source code
get_fasta_filename Man page Source code
get_file_base_sans_ext Source code
get_freq_equilibrium_names Source code
get_gamma_site_model_n_distrs Man page Source code
get_gamma_site_model_n_params Source code
get_has_non_strict_clock_model Source code
get_n_taxa Source code
get_operator_id_pre Source code
get_param_names Source code
get_phylo_crown_age Source code
get_site_model_n_distrs Source code
get_site_model_n_params Source code
get_site_model_names Source code
get_site_models_n_distrs Source code
get_site_models_n_params Source code
get_taxa_names Man page Source code
get_tree_prior_n_distrs Source code
get_tree_prior_n_params Source code
get_tree_prior_names Source code
get_tree_priors_n_distrs Source code
get_tree_priors_n_params Source code
get_xml_closing_tag Source code
get_xml_opening_tag Source code
has_xml_closing_tag Source code
has_xml_opening_tag Source code
has_xml_short_closing_tag Source code
indent Source code
init_bd_tree_prior Man page Source code
init_ccp_tree_prior Man page Source code
init_cep_tree_prior Man page Source code
init_clock_models Source code
init_distr Source code
init_gamma_site_model Source code
init_gtr_site_model Man page Source code
init_hky_site_model Man page Source code
init_jc69_site_model Man page Source code
init_mrca_priors Source code
init_param Source code
init_rln_clock_model Man page Source code
init_site_models Source code
init_strict_clock_model Man page Source code
init_tn93_site_model Man page Source code
init_tree_priors Source code
init_yule_tree_prior Man page Source code
interspace Source code
is_alpha_param Source code
is_bd_tree_prior Source code
is_beta_distr Source code
is_beta_param Source code
is_cbs_tree_prior Source code
is_ccp_tree_prior Source code
is_cep_tree_prior Source code
is_clock_model Source code
is_clock_model_name Source code
is_clock_rate_param Source code
is_default_mcmc Source code
is_distr Source code
is_distr_name Source code
is_exp_distr Source code
is_freq_equilibrium_name Source code
is_gamma_distr Source code
is_gamma_site_model Source code
is_gtr_site_model Source code
is_hky_site_model Source code
is_id Source code
is_in_patterns Source code
is_init_bd_tree_prior Source code
is_init_beta_distr Man page Source code
is_init_cbs_tree_prior Source code
is_init_ccp_tree_prior Source code
is_init_cep_tree_prior Man page Source code
is_init_clock_model Source code
is_init_distr Source code
is_init_exp_distr Man page Source code
is_init_gamma_distr Man page Source code
is_init_gamma_site_model Source code
is_init_gtr_site_model Source code
is_init_hky_site_model Source code
is_init_inv_gamma_distr Man page Source code
is_init_jc69_site_model Source code
is_init_laplace_distr Man page Source code
is_init_log_normal_distr Man page Source code
is_init_mrca_prior Source code
is_init_normal_distr Man page Source code
is_init_one_div_x_distr Man page Source code
is_init_param Source code
is_init_poisson_distr Man page Source code
is_init_rln_clock_model Source code
is_init_site_model Source code
is_init_strict_clock_model Source code
is_init_tn93_site_model Source code
is_init_tree_prior Source code
is_init_uniform_distr Man page Source code
is_init_yule_tree_prior Source code
is_inv_gamma_distr Source code
is_jc69_site_model Source code
is_kappa_1_param Source code
is_kappa_2_param Source code
is_lambda_param Source code
is_laplace_distr Source code
is_log_normal_distr Source code
is_m_param Source code
is_mcmc Source code
is_mcmc_nested_sampling Source code
is_mean_param Source code
is_misc_options Source code
is_mrca_prior Source code
is_mrca_prior_with_distr Source code
is_mu_param Source code
is_normal_distr Source code
is_one_div_x_distr Source code
is_one_na Source code
is_param Source code
is_param_name Source code
is_phylo Source code
is_poisson_distr Source code
is_rate_ac_param Source code
is_rate_ag_param Source code
is_rate_at_param Source code
is_rate_cg_param Source code
is_rate_ct_param Source code
is_rate_gt_param Source code
is_rln_clock_model Source code
is_s_param Source code
is_scale_param Source code
is_sigma_param Source code
is_site_model Source code
is_site_model_name Source code
is_strict_clock_model Source code
is_tn93_site_model Source code
is_tree_prior Source code
is_tree_prior_name Source code
is_uniform_distr Source code
is_xml Source code
is_yule_tree_prior Source code
mcmc_to_xml_run Source code
mcmc_to_xml_run_default Source code
mcmc_to_xml_run_nested_sampling Source code
mrca_prior_to_xml_lh_distr Source code
mrca_prior_to_xml_prior_distr Source code
mrca_prior_to_xml_state Source code
mrca_prior_to_xml_taxonset Source code
mrca_prior_to_xml_tracelog Source code
mrca_priors_to_xml_prior_distr Source code
mrca_priors_to_xml_state Source code
mrca_priors_to_xml_tracelog Source code
no_taxa_to_xml_tree Source code
parameter_to_xml Source code
parameter_to_xml_alpha Man page Source code
parameter_to_xml_beta Man page Source code
parameter_to_xml_clock_rate Man page Source code
parameter_to_xml_kappa_1 Man page Source code
parameter_to_xml_kappa_2 Man page Source code
parameter_to_xml_lambda Man page Source code
parameter_to_xml_m Man page Source code
parameter_to_xml_mean Man page Source code
parameter_to_xml_mu Man page Source code
parameter_to_xml_rate_ac Man page Source code
parameter_to_xml_rate_ag Man page Source code
parameter_to_xml_rate_at Man page Source code
parameter_to_xml_rate_cg Man page Source code
parameter_to_xml_rate_ct Man page Source code
parameter_to_xml_rate_gt Man page Source code
parameter_to_xml_s Man page Source code
parameter_to_xml_scale Man page Source code
parameter_to_xml_sigma Man page Source code
phylo_to_xml_state Source code
remove_empty_lines Source code
remove_multiline Source code
rln_clock_model_to_xml_mean_rate_prior Source code
rnd_phylo_to_xml_init Source code
site_model_to_xml_lh_distr Source code
site_model_to_xml_operators Source code
site_model_to_xml_prior_distr Source code
site_model_to_xml_state Source code
site_model_to_xml_subst_model Source code
site_model_to_xml_tracelog Source code
site_models_to_xml_operators Source code
site_models_to_xml_prior_distr Source code
site_models_to_xml_state Source code
site_models_to_xml_tracelog Source code
taxa_to_xml_tree Source code
tipdate_taxa_to_xml_tree Source code
tree_models_to_xml_tracelog Source code
tree_prior_to_xml_operators Source code
tree_prior_to_xml_prior_distr Source code
tree_prior_to_xml_state Source code
tree_prior_to_xml_tracelog Source code
tree_priors_to_xml_operators Source code
tree_priors_to_xml_prior_distr Source code
tree_priors_to_xml_state Source code
tree_priors_to_xml_tracelog Source code
yule_tree_prior_to_xml_prior_distr Man page Source code
richelbilderbeek/beautier documentation built on Dec. 10, 2018, 2:06 p.m.