are_clock_models	are_clock_models
are_equal_mcmcs	are_equal_mcmcs
are_equal_screenlogs	are_equal_screenlogs
are_equal_tracelogs	are_equal_tracelogs
are_equal_treelogs	are_equal_treelogs
are_equal_xml_files	are_equal_xml_files
are_equal_xml_lines	are_equal_xml_lines
are_equivalent_xml_files	are_equivalent_xml_files
are_equivalent_xml_lines	are_equivalent_xml_lines
are_equivalent_xml_lines_all	are_equivalent_xml_lines_all
are_equivalent_xml_lines_loggers	are_equivalent_xml_lines_loggers
are_equivalent_xml_lines_operators	are_equivalent_xml_lines_operators
are_equivalent_xml_lines_section	are_equivalent_xml_lines_section
are_fasta_filenames	are_fasta_filenames
are_ids	are_ids
are_init_clock_models	are_init_clock_models
are_init_mrca_priors	are_init_mrca_priors
are_init_site_models	are_init_site_models
are_init_tree_priors	are_init_tree_priors
are_mrca_align_ids_in_fasta	are_mrca_align_ids_in_fasta
are_mrca_priors	are_mrca_priors
are_mrca_taxon_names_in_fasta	are_mrca_taxon_names_in_fasta
are_rln_clock_models	are_rln_clock_models
are_site_models	are_site_models
are_tree_priors	are_tree_priors
bd_tree_prior_to_xml_prior_distr	bd_tree_prior_to_xml_prior_distr
beautier	beautier
cbs_tree_prior_to_xml_prior_distr	cbs_tree_prior_to_xml_prior_distr
ccp_tree_prior_to_xml_prior_distr	ccp_tree_prior_to_xml_prior_distr
cep_tree_prior_to_xml_prior_distr	cep_tree_prior_to_xml_prior_distr
check_alignment_id	check_alignment_id
check_beauti_options	check_beauti_options
check_clock_model	check_clock_model
check_clock_models	check_clock_models
check_file_and_model_agree	check_file_and_model_agree
check_file_exists	check_file_exists
check_gamma_site_model	check_gamma_site_model
check_gamma_site_model_names	check_gamma_site_model_names
check_gtr_site_model	check_gtr_site_model
check_gtr_site_model_names	check_gtr_site_model_names
check_inference_model	check_inference_model
check_inference_models	check_inference_models
check_is_monophyletic	check_is_monophyletic
check_log_mode	check_log_mode
check_log_sort	check_log_sort
check_mcmc	check_mcmc
check_mcmc_list_element_names	check_mcmc_list_element_names
check_mcmc_nested_sampling	check_ns_mcmc
check_mcmc_values	check_mcmc_values
check_mrca_prior	check_mrca_prior
check_mrca_prior_name	check_mrca_prior_name
check_mrca_prior_names	check_mrca_prior_names
check_mrca_prior_taxa_names	check_mrca_prior_taxa_names
check_nested_sampling_mcmc	check_ns_mcmc
check_ns_mcmc	check_ns_mcmc
check_param	check_param
check_param_names	check_param_names
check_param_types	check_param_types
check_phylogeny	check_phylogeny
check_rename_fun	check_rename_fun
check_rln_clock_model	check_rln_clock_model
check_screenlog	check_screenlog
check_screenlog_names	check_screenlog_names
check_screenlog_values	check_screenlog_values
check_site_model	check_site_model
check_site_models	check_site_models
check_site_model_names	check_site_model_names
check_site_model_types	check_site_model_types
check_store_every	check_store_every
check_strict_clock_model	check_strict_clock_model
check_tn93_site_model	check_tn93_site_model
check_tn93_site_model_names	check_tn93_site_model_names
check_tracelog	check_tracelog
check_tracelog_names	check_tracelog_names
check_tracelog_values	check_tracelog_values
check_treelog	check_treelog
check_treelog_names	check_treelog_names
check_treelog_values	check_treelog_values
check_tree_prior	check_tree_prior
check_tree_priors	check_tree_priors
clock_models_to_xml_operators	clock_models_to_xml_operators
clock_models_to_xml_prior_distr	clock_models_to_xml_prior_distr
clock_models_to_xml_state	clock_models_to_xml_state
clock_models_to_xml_tracelog	clock_models_to_xml_tracelog
clock_model_to_xml_lh_distr	clock_model_to_xml_lh_distr
clock_model_to_xml_operators	clock_model_to_xml_operators
clock_model_to_xml_prior_distr	clock_model_to_xml_prior_distr
clock_model_to_xml_state	clock_model_to_xml_state
clock_model_to_xml_tracelog	clock_model_to_xml_tracelog
clock_model_to_xml_treelogger	clock_model_to_xml_treelogger
compare_lines	compare_lines
count_trailing_spaces	count_trailing_spaces
create_alpha_param	create_alpha_param
create_bd_tree_prior	create_bd_tree_prior
create_beast2_beast_xml	create_beast2_beast_xml
create_beast2_input	create_beast2_input
create_beast2_input_beast	create_beast2_input_beast
create_beast2_input_data	create_beast2_input_data
create_beast2_input_data_sequences	create_beast2_input_data_sequences
create_beast2_input_distr	create_beast2_input_distr
create_beast2_input_distr_lh	create_beast2_input_distr_lh
create_beast2_input_distr_prior	create_beast2_input_distr_prior
create_beast2_input_file	create_beast2_input_file
create_beast2_input_file_from_model	create_beast2_input_file_from_model
create_beast2_input_from_model	create_beast2_input_from_model
create_beast2_input_init	create_beast2_input_init
create_beast2_input_map	create_beast2_input_map
create_beast2_input_operators	create_beast2_input_operators
create_beast2_input_run	create_beast2_input_run
create_beast2_input_state	create_beast2_input_state
create_beauti_options	create_beauti_options
create_beta_distr	create_beta_distr
create_beta_param	create_beta_param
create_cbs_tree_prior	create_cbs_tree_prior
create_ccp_tree_prior	create_ccp_tree_prior
create_cep_tree_prior	create_cep_tree_prior
create_clock_model	create_clock_model
create_clock_models	create_clock_models
create_clock_models_from_names	create_clock_models_from_names
create_clock_model_from_name	create_clock_model_from_name
create_clock_model_rln	create_rln_clock_model
create_clock_model_strict	create_strict_clock_model
create_clock_rate_param	create_clock_rate_param
create_data_xml	create_data_xml
create_distr	create_distr
create_distr_beta	create_beta_distr
create_distr_exp	create_exp_distr
create_distr_gamma	create_gamma_distr
create_distr_inv_gamma	create_inv_gamma_distr
create_distr_laplace	create_laplace_distr
create_distr_log_normal	create_log_normal_distr
create_distr_normal	create_normal_distr
create_distr_one_div_x	create_one_div_x_distr
create_distr_poisson	create_poisson_distr
create_distr_uniform	create_uniform_distr
create_exp_distr	create_exp_distr
create_gamma_distr	create_gamma_distr
create_gamma_site_model	create_gamma_site_model
create_gtr_site_model	create_gtr_site_model
create_hky_site_model	create_hky_site_model
create_inference_model	create_inference_model
create_inv_gamma_distr	create_inv_gamma_distr
create_jc69_site_model	create_jc69_site_model
create_kappa_1_param	create_kappa_1_param
create_kappa_2_param	create_kappa_2_param
create_lambda_param	create_lambda_param
create_laplace_distr	create_laplace_distr
create_loggers_xml	create_loggers_xml
create_log_normal_distr	create_log_normal_distr
create_mcmc	create_mcmc
create_mcmc_nested_sampling	create_ns_mcmc
create_mean_param	create_mean_param
create_mrca_prior	create_mrca_prior
create_mu_param	create_mu_param
create_m_param	create_m_param
create_normal_distr	create_normal_distr
create_ns_mcmc	create_ns_mcmc
create_one_div_x_distr	create_one_div_x_distr
create_param	create_param
create_param_alpha	create_alpha_param
create_param_beta	create_beta_param
create_param_clock_rate	create_clock_rate_param
create_param_kappa_1	create_kappa_1_param
create_param_kappa_2	create_kappa_2_param
create_param_lambda	create_lambda_param
create_param_m	create_m_param
create_param_mean	create_mean_param
create_param_mu	create_mu_param
create_param_rate_ac	create_rate_ac_param
create_param_rate_ag	create_rate_ag_param
create_param_rate_at	create_rate_at_param
create_param_rate_cg	create_rate_cg_param
create_param_rate_ct	create_rate_ct_param
create_param_rate_gt	create_rate_gt_param
create_param_s	create_s_param
create_param_scale	create_scale_param
create_param_sigma	create_sigma_param
create_poisson_distr	create_poisson_distr
create_rate_ac_param	create_rate_ac_param
create_rate_ag_param	create_rate_ag_param
create_rate_at_param	create_rate_at_param
create_rate_cg_param	create_rate_cg_param
create_rate_ct_param	create_rate_ct_param
create_rate_gt_param	create_rate_gt_param
create_rln_clock_model	create_rln_clock_model
create_scale_param	create_scale_param
create_screenlog	create_screenlog
create_screenlog_xml	create_screenlog_xml
create_sigma_param	create_sigma_param
create_site_model	create_site_model
create_site_models	create_site_models
create_site_models_from_names	create_site_models_from_names
create_site_model_from_name	create_site_model_from_name
create_site_model_gtr	create_gtr_site_model
create_site_model_hky	create_hky_site_model
create_site_model_jc69	create_jc69_site_model
create_site_model_tn93	create_tn93_site_model
create_strict_clock_model	create_strict_clock_model
create_s_param	create_s_param
create_temp_screenlog_filename	create_temp_screenlog_filename
create_temp_tracelog_filename	create_temp_tracelog_filename
create_temp_treelog_filename	create_temp_treelog_filename
create_test_inference_model	create_test_inference_model
create_test_mcmc	create_test_mcmc
create_test_ns_inference_model	create_test_ns_inference_model
create_test_ns_mcmc	create_test_ns_mcmc
create_test_screenlog	create_test_screenlog
create_test_tracelog	create_test_tracelog
create_test_treelog	create_test_treelog
create_tn93_site_model	create_tn93_site_model
create_tracelog	create_tracelog
create_tracelog_xml	create_tracelog_xml
create_trait_set_string	create_trait_set_string
create_treelog	create_treelog
create_treelog_xml	create_treelog_xml
create_tree_prior	create_tree_prior
create_tree_priors	create_tree_priors
create_tree_prior_bd	create_bd_tree_prior
create_tree_prior_cbs	create_cbs_tree_prior
create_tree_prior_ccp	create_ccp_tree_prior
create_tree_prior_cep	create_cep_tree_prior
create_tree_prior_yule	create_yule_tree_prior
create_uniform_distr	create_uniform_distr
create_xml_declaration	create_xml_declaration
create_yule_tree_prior	create_yule_tree_prior
default_parameters_doc	default_parameters_doc
default_params_doc	default_params_doc
distr_to_xml	distr_to_xml
distr_to_xml_beta	distr_to_xml_beta
distr_to_xml_exp	distr_to_xml_exp
distr_to_xml_gamma	distr_to_xml_gamma
distr_to_xml_inv_gamma	distr_to_xml_inv_gamma
distr_to_xml_laplace	distr_to_xml_laplace
distr_to_xml_log_normal	distr_to_xml_log_normal
distr_to_xml_normal	distr_to_xml_normal
distr_to_xml_one_div_x	distr_to_xml_one_div_x
distr_to_xml_poisson	distr_to_xml_poisson
distr_to_xml_uniform	distr_to_xml_uniform
extract_xml_loggers_from_lines	extract_xml_loggers_from_lines
extract_xml_operators_from_lines	extract_xml_operators_from_lines
extract_xml_section_from_lines	extract_xml_section_from_lines
fasta_file_to_sequences	fasta_file_to_sequences
find_clock_model	find_clock_model
find_first_regex_line	find_first_regex_line
find_first_xml_opening_tag_line	find_first_xml_opening_tag_line
find_last_regex_line	find_last_regex_line
find_last_xml_closing_tag_line	find_last_xml_closing_tag_line
freq_equilibrium_to_xml	freq_equilibrium_to_xml
gamma_site_models_to_xml_prior_distr	gamma_site_models_to_xml_prior_distr
gamma_site_model_to_xml_prior_distr	gamma_site_model_to_xml_prior_distr
gamma_site_model_to_xml_state	gamma_site_model_to_xml_state
get_alignment_id	get_alignment_id
get_alignment_ids	get_alignment_ids
get_alignment_ids_from_fasta_filenames	get_alignment_ids_from_fasta_filenames
get_beautier_path	get_beautier_path
get_beautier_paths	get_beautier_paths
get_clock_models_ids	get_clock_models_ids
get_clock_model_name	get_clock_model_name
get_clock_model_names	get_clock_model_names
get_crown_age	get_crown_age
get_distr_names	get_distr_names
get_distr_n_params	get_distr_n_params
get_fasta_filename	get_fasta_filename
get_file_base_sans_ext	get_file_base_sans_ext
get_freq_equilibrium_names	get_freq_equilibrium_names
get_gamma_site_model_n_distrs	get_gamma_site_model_n_distrs
get_gamma_site_model_n_params	get_gamma_site_model_n_params
get_has_non_strict_clock_model	get_has_non_strict_clock_model
get_inference_model_filenames	get_inference_model_filenames
get_log_modes	get_log_modes
get_log_sorts	get_log_sorts
get_mcmc_filenames	get_mcmc_filenames
get_n_taxa	get_n_taxa
get_operator_id_pre	get_operator_id_pre
get_param_names	get_param_names
get_remove_dir_fun	get_remove_dir_fun
get_remove_hex_fun	get_remove_hex_fun
get_replace_dir_fun	get_replace_dir_fun
get_site_models_n_distrs	get_site_models_n_distrs
get_site_models_n_params	get_site_models_n_params
get_site_model_names	get_site_model_names
get_site_model_n_distrs	get_site_model_n_distrs
get_site_model_n_params	get_site_model_n_params
get_taxa_names	get_taxa_names
get_tree_priors_n_distrs	get_tree_priors_n_distrs
get_tree_priors_n_params	get_tree_priors_n_params
get_tree_prior_names	get_tree_prior_names
get_tree_prior_n_distrs	get_tree_prior_n_distrs
get_tree_prior_n_params	get_tree_prior_n_params
get_xml_closing_tag	get_xml_closing_tag
get_xml_opening_tag	get_xml_opening_tag
gtr_site_model_to_xml_subst_model	gtr_site_model_to_xml_subst_model
has_mrca_prior	has_mrca_prior
has_xml_closing_tag	has_xml_closing_tag
has_xml_opening_tag	has_xml_opening_tag
has_xml_short_closing_tag	has_xml_short_closing_tag
hky_site_model_to_xml_subst_model	hky_site_model_to_xml_subst_model
indent	indent
init_bd_tree_prior	init_bd_tree_prior
init_beta_distr	init_beta_distr
init_ccp_tree_prior	init_ccp_tree_prior
init_cep_tree_prior	init_cep_tree_prior
init_clock_models	init_clock_models
init_distr	init_distr
init_exp_distr	init_exp_distr
init_gamma_distr	init_gamma_distr
init_gamma_site_model	init_gamma_site_model
init_gtr_site_model	init_gtr_site_model
init_hky_site_model	init_hky_site_model
init_inference_model	init_inference_model
init_inv_gamma_distr	init_inv_gamma_distr
init_jc69_site_model	init_jc69_site_model
init_laplace_distr	init_laplace_distr
init_log_normal_distr	init_log_normal_distr
init_mrca_prior	init_mrca_prior
init_mrca_priors	init_mrca_priors
init_normal_distr	init_normal_distr
init_one_div_x_distr	init_one_div_x_distr
init_param	init_param
init_poisson_distr	init_poisson_distr
init_rln_clock_model	init_rln_clock_model
init_site_models	init_site_models
init_strict_clock_model	init_strict_clock_model
init_tn93_site_model	init_tn93_site_model
init_tree_priors	init_tree_priors
init_uniform_distr	init_uniform_distr
init_yule_tree_prior	init_yule_tree_prior
interspace	interspace
is_alpha_param	is_alpha_param
is_bd_tree_prior	is_bd_tree_prior
is_beauti_options	is_beauti_options
is_beta_distr	is_beta_distr
is_beta_param	is_beta_param
is_cbs_tree_prior	is_cbs_tree_prior
is_ccp_tree_prior	is_ccp_tree_prior
is_cep_tree_prior	is_cep_tree_prior
is_clock_model	is_clock_model
is_clock_model_name	is_clock_model_name
is_clock_rate_param	is_clock_rate_param
is_default_mcmc	is_default_mcmc
is_distr	is_distr
is_distr_name	is_distr_name
is_exp_distr	is_exp_distr
is_freq_equilibrium_name	is_freq_equilibrium_name
is_gamma_distr	is_gamma_distr
is_gamma_site_model	is_gamma_site_model
is_gtr_site_model	is_gtr_site_model
is_hky_site_model	is_hky_site_model
is_id	is_id
is_inference_model	is_inference_model
is_init_bd_tree_prior	is_init_bd_tree_prior
is_init_beta_distr	is_init_beta_distr
is_init_cbs_tree_prior	is_init_cbs_tree_prior
is_init_ccp_tree_prior	is_init_ccp_tree_prior
is_init_cep_tree_prior	is_init_cep_tree_prior
is_init_clock_model	is_init_clock_model
is_init_distr	is_init_distr
is_init_exp_distr	is_init_exp_distr
is_init_gamma_distr	is_init_gamma_distr
is_init_gamma_site_model	is_init_gamma_site_model
is_init_gtr_site_model	is_init_gtr_site_model
is_init_hky_site_model	is_init_hky_site_model
is_init_inv_gamma_distr	is_init_inv_gamma_distr
is_init_jc69_site_model	is_init_jc69_site_model
is_init_laplace_distr	is_init_laplace_distr
is_init_log_normal_distr	is_init_log_normal_distr
is_init_mrca_prior	is_init_mrca_prior
is_init_normal_distr	is_init_normal_distr
is_init_one_div_x_distr	is_init_one_div_x_distr
is_init_param	is_init_param
is_init_poisson_distr	is_init_poisson_distr
is_init_rln_clock_model	is_init_rln_clock_model
is_init_site_model	is_init_site_model
is_init_strict_clock_model	is_init_strict_clock_model
is_init_tn93_site_model	is_init_tn93_site_model
is_init_tree_prior	is_init_tree_prior
is_init_uniform_distr	is_init_uniform_distr
is_init_yule_tree_prior	is_init_yule_tree_prior
is_inv_gamma_distr	is_inv_gamma_distr
is_in_patterns	is_in_patterns
is_jc69_site_model	is_jc69_site_model
is_kappa_1_param	is_kappa_1_param
is_kappa_2_param	is_kappa_2_param
is_lambda_param	is_lambda_param
is_laplace_distr	is_laplace_distr
is_log_normal_distr	is_log_normal_distr
is_mcmc	is_mcmc
is_mcmc_nested_sampling	is_mcmc_nested_sampling
is_mean_param	is_mean_param
is_mrca_align_ids_in_fastas	is_mrca_align_ids_in_fastas
is_mrca_align_id_in_fasta	is_mrca_align_id_in_fasta
is_mrca_prior	is_mrca_prior
is_mrca_prior_with_distr	is_mrca_prior_with_distr
is_mu_param	is_mu_param
is_m_param	is_m_param
is_nested_sampling_mcmc	is_mcmc_nested_sampling
is_normal_distr	is_normal_distr
is_one_bool	is_one_bool
is_one_div_x_distr	is_one_div_x_distr
is_one_double	is_one_double
is_one_int	is_one_int
is_one_na	is_one_na
is_param	is_param
is_param_name	is_param_name
is_phylo	is_phylo
is_poisson_distr	is_poisson_distr
is_rate_ac_param	is_rate_ac_param
is_rate_ag_param	is_rate_ag_param
is_rate_at_param	is_rate_at_param
is_rate_cg_param	is_rate_cg_param
is_rate_ct_param	is_rate_ct_param
is_rate_gt_param	is_rate_gt_param
is_rln_clock_model	is_rln_clock_model
is_scale_param	is_scale_param
is_sigma_param	is_sigma_param
is_site_model	is_site_model
is_site_model_name	is_site_model_name
is_strict_clock_model	is_strict_clock_model
is_s_param	is_s_param
is_tn93_site_model	is_tn93_site_model
is_tree_prior	is_tree_prior
is_tree_prior_name	is_tree_prior_name
is_uniform_distr	is_uniform_distr
is_xml	is_xml
is_yule_tree_prior	is_yule_tree_prior
jc69_site_model_to_xml_subst_model	jc69_site_model_to_xml_subst_model
mcmc_to_xml_run	mcmc_to_xml_run
mcmc_to_xml_run_default	mcmc_to_xml_run_default
mcmc_to_xml_run_nested_sampling	mcmc_to_xml_run_nested_sampling
mrca_priors_to_xml_prior_distr	mrca_priors_to_xml_prior_distr
mrca_priors_to_xml_state	mrca_priors_to_xml_state
mrca_priors_to_xml_tracelog	mrca_priors_to_xml_tracelog
mrca_prior_to_xml_lh_distr	mrca_prior_to_xml_lh_distr
mrca_prior_to_xml_prior_distr	mrca_prior_to_xml_prior_distr
mrca_prior_to_xml_state	mrca_prior_to_xml_state
mrca_prior_to_xml_taxonset	mrca_prior_to_xml_taxonset
mrca_prior_to_xml_tracelog	mrca_prior_to_xml_tracelog
no_taxa_to_xml_tree	no_taxa_to_xml_tree
parameter_to_xml	parameter_to_xml
parameter_to_xml_alpha	parameter_to_xml_alpha
parameter_to_xml_beta	parameter_to_xml_beta
parameter_to_xml_clock_rate	parameter_to_xml_clock_rate
parameter_to_xml_kappa_1	parameter_to_xml_kappa_1
parameter_to_xml_kappa_2	parameter_to_xml_kappa_2
parameter_to_xml_lambda	parameter_to_xml_lambda
parameter_to_xml_m	parameter_to_xml_m
parameter_to_xml_mean	parameter_to_xml_mean
parameter_to_xml_mu	parameter_to_xml_mu
parameter_to_xml_rate_ac	parameter_to_xml_rate_ac
parameter_to_xml_rate_ag	parameter_to_xml_rate_ag
parameter_to_xml_rate_at	parameter_to_xml_rate_at
parameter_to_xml_rate_cg	parameter_to_xml_rate_cg
parameter_to_xml_rate_ct	parameter_to_xml_rate_ct
parameter_to_xml_rate_gt	parameter_to_xml_rate_gt
parameter_to_xml_s	parameter_to_xml_s
parameter_to_xml_scale	parameter_to_xml_scale
parameter_to_xml_sigma	parameter_to_xml_sigma
phylo_to_xml_state	phylo_to_xml_state
remove_empty_lines	remove_empty_lines
remove_multiline	remove_multiline
rename_inference_model_filenames	rename_inference_model_filenames
rename_mcmc_filenames	rename_mcmc_filenames
rln_clock_model_to_xml_mean_rate_prior	rln_clock_model_to_xml_mean_rate_prior
rnd_phylo_to_xml_init	rnd_phylo_to_xml_init
site_models_to_xml_operators	site_models_to_xml_operators
site_models_to_xml_prior_distr	site_models_to_xml_prior_distr
site_models_to_xml_state	site_models_to_xml_state
site_models_to_xml_tracelog	site_models_to_xml_tracelog
site_model_to_xml_lh_distr	site_model_to_xml_lh_distr
site_model_to_xml_operators	site_model_to_xml_operators
site_model_to_xml_prior_distr	site_model_to_xml_prior_distr
site_model_to_xml_state	site_model_to_xml_state
site_model_to_xml_subst_model	site_model_to_xml_subst_model
site_model_to_xml_tracelog	site_model_to_xml_tracelog
taxa_to_xml_tree	taxa_to_xml_tree
tipdate_taxa_to_xml_tree	tipdate_taxa_to_xml_tree
tn93_site_model_to_xml_subst_model	tn93_site_model_to_xml_subst_model
tree_models_to_xml_tracelog	tree_models_to_xml_tracelog
tree_priors_to_xml_operators	tree_priors_to_xml_operators
tree_priors_to_xml_prior_distr	tree_priors_to_xml_prior_distr
tree_priors_to_xml_state	tree_priors_to_xml_state
tree_priors_to_xml_tracelog	tree_priors_to_xml_tracelog
tree_prior_to_xml_operators	tree_prior_to_xml_operators
tree_prior_to_xml_prior_distr	tree_prior_to_xml_prior_distr
tree_prior_to_xml_state	tree_prior_to_xml_state
tree_prior_to_xml_tracelog	tree_prior_to_xml_tracelog
yule_tree_prior_to_xml_prior_distr	yule_tree_prior_to_xml_prior_distr
