[console_scripts]
phykit = phykit.phykit:main
pk_al = phykit.phykit:alignment_length
pk_alignment_entropy = phykit.phykit:alignment_entropy
pk_alignment_length = phykit.phykit:alignment_length
pk_alignment_length_no_gaps = phykit.phykit:alignment_length_no_gaps
pk_alignment_outlier_taxa = phykit.phykit:alignment_outlier_taxa
pk_alignment_recoding = phykit.phykit:alignment_recoding
pk_aln_entropy = phykit.phykit:alignment_entropy
pk_aln_len = phykit.phykit:alignment_length
pk_aln_len_no_gaps = phykit.phykit:alignment_length_no_gaps
pk_aln_recoding = phykit.phykit:alignment_recoding
pk_alng = phykit.phykit:alignment_length_no_gaps
pk_anc_recon = phykit.phykit:ancestral_state_reconstruction
pk_ancestral_state_reconstruction = phykit.phykit:ancestral_state_reconstruction
pk_aot = phykit.phykit:alignment_outlier_taxa
pk_asr = phykit.phykit:ancestral_state_reconstruction
pk_bipartition_support_stats = phykit.phykit:bipartition_support_stats
pk_blm = phykit.phykit:branch_length_multiplier
pk_branch_length_multiplier = phykit.phykit:branch_length_multiplier
pk_brownie = phykit.phykit:rate_heterogeneity
pk_bss = phykit.phykit:bipartition_support_stats
pk_casr = phykit.phykit:concordance_asr
pk_cb = phykit.phykit:collapse_branches
pk_cbps = phykit.phykit:compositional_bias_per_site
pk_cc = phykit.phykit:create_concatenation_matrix
pk_clan_check = phykit.phykit:hidden_paralogy_check
pk_cmap = phykit.phykit:cont_map
pk_collapse = phykit.phykit:collapse_branches
pk_collapse_branches = phykit.phykit:collapse_branches
pk_column_score = phykit.phykit:column_score
pk_comp_bias_per_site = phykit.phykit:compositional_bias_per_site
pk_comp_tax = phykit.phykit:composition_per_taxon
pk_comp_taxon = phykit.phykit:composition_per_taxon
pk_composition_per_taxon = phykit.phykit:composition_per_taxon
pk_compositional_bias_per_site = phykit.phykit:compositional_bias_per_site
pk_conc_asr = phykit.phykit:concordance_asr
pk_concordance_asr = phykit.phykit:concordance_asr
pk_consensus = phykit.phykit:consensus_tree
pk_consensus_network = phykit.phykit:consensus_network
pk_consensus_tree = phykit.phykit:consensus_tree
pk_consnet = phykit.phykit:consensus_network
pk_cont_map = phykit.phykit:cont_map
pk_contmap = phykit.phykit:cont_map
pk_cophylo = phykit.phykit:cophylo
pk_covarying_evolutionary_rates = phykit.phykit:covarying_evolutionary_rates
pk_cover = phykit.phykit:covarying_evolutionary_rates
pk_create_concat = phykit.phykit:create_concatenation_matrix
pk_create_concatenation_matrix = phykit.phykit:create_concatenation_matrix
pk_cs = phykit.phykit:column_score
pk_ctree = phykit.phykit:consensus_tree
pk_da = phykit.phykit:discordance_asymmetry
pk_degree_of_violation_of_a_molecular_clock = phykit.phykit:dvmc
pk_density_map = phykit.phykit:density_map
pk_densitymap = phykit.phykit:density_map
pk_detect_shifts = phykit.phykit:ou_shift_detection
pk_dimreduce = phykit.phykit:phylogenetic_ordination
pk_disc_asym = phykit.phykit:discordance_asymmetry
pk_discordance_asymmetry = phykit.phykit:discordance_asymmetry
pk_dmap = phykit.phykit:density_map
pk_dvmc = phykit.phykit:dvmc
pk_entropy = phykit.phykit:alignment_entropy
pk_erps = phykit.phykit:evolutionary_rate_per_site
pk_etm = phykit.phykit:evo_tempo_map
pk_evo_rate = phykit.phykit:evolutionary_rate
pk_evo_rate_per_site = phykit.phykit:evolutionary_rate_per_site
pk_evo_tempo_map = phykit.phykit:evo_tempo_map
pk_evolutionary_rate = phykit.phykit:evolutionary_rate
pk_evolutionary_rate_per_site = phykit.phykit:evolutionary_rate_per_site
pk_faidx = phykit.phykit:faidx
pk_fc = phykit.phykit:fit_continuous
pk_fd = phykit.phykit:fit_discrete
pk_fit_continuous = phykit.phykit:fit_continuous
pk_fit_discrete = phykit.phykit:fit_discrete
pk_fit_ouwie = phykit.phykit:ouwie
pk_fitcontinuous = phykit.phykit:fit_continuous
pk_fitdiscrete = phykit.phykit:fit_discrete
pk_gamma = phykit.phykit:ltt
pk_gamma_stat = phykit.phykit:ltt
pk_gc = phykit.phykit:gc_content
pk_gc_content = phykit.phykit:gc_content
pk_ge = phykit.phykit:faidx
pk_get_entry = phykit.phykit:faidx
pk_hidden_paralogy_check = phykit.phykit:hidden_paralogy_check
pk_ibs = phykit.phykit:internal_branch_stats
pk_il = phykit.phykit:internode_labeler
pk_internal_branch_stats = phykit.phykit:internal_branch_stats
pk_internode_labeler = phykit.phykit:internode_labeler
pk_is_monophyletic = phykit.phykit:monophyly_check
pk_kf = phykit.phykit:kf_distance
pk_kf_dist = phykit.phykit:kf_distance
pk_kf_distance = phykit.phykit:kf_distance
pk_kuhner_felsenstein_distance = phykit.phykit:kf_distance
pk_l1ou = phykit.phykit:ou_shift_detection
pk_labels = phykit.phykit:tip_labels
pk_last_common_ancestor_subtree = phykit.phykit:last_common_ancestor_subtree
pk_lb_score = phykit.phykit:lb_score
pk_lbs = phykit.phykit:lb_score
pk_lca_subtree = phykit.phykit:last_common_ancestor_subtree
pk_long_branch_score = phykit.phykit:lb_score
pk_ltt = phykit.phykit:ltt
pk_mask = phykit.phykit:mask_alignment
pk_mask_alignment = phykit.phykit:mask_alignment
pk_mask_aln = phykit.phykit:mask_alignment
pk_monophyly_check = phykit.phykit:monophyly_check
pk_multi_regime_ou = phykit.phykit:ouwie
pk_nanuq = phykit.phykit:quartet_network
pk_nearest_neighbor_interchange = phykit.phykit:nearest_neighbor_interchange
pk_net_signal = phykit.phykit:network_signal
pk_netsig = phykit.phykit:network_signal
pk_network_signal = phykit.phykit:network_signal
pk_nni = phykit.phykit:nearest_neighbor_interchange
pk_occ_tax = phykit.phykit:occupancy_per_taxon
pk_occupancy_per_taxon = phykit.phykit:occupancy_per_taxon
pk_occupancy_taxon = phykit.phykit:occupancy_per_taxon
pk_ord = phykit.phykit:phylogenetic_ordination
pk_ordination = phykit.phykit:phylogenetic_ordination
pk_ou_shift_detection = phykit.phykit:ou_shift_detection
pk_ou_shifts = phykit.phykit:ou_shift_detection
pk_outlier_taxa = phykit.phykit:alignment_outlier_taxa
pk_ouwie = phykit.phykit:ouwie
pk_p2n = phykit.phykit:thread_dna
pk_pairwise_id = phykit.phykit:pairwise_identity
pk_pairwise_identity = phykit.phykit:pairwise_identity
pk_pal2nal = phykit.phykit:thread_dna
pk_paqc = phykit.phykit:plot_alignment_qc
pk_parsimony_informative_sites = phykit.phykit:parsimony_informative_sites
pk_patristic_distances = phykit.phykit:patristic_distances
pk_pd = phykit.phykit:patristic_distances
pk_pdr = phykit.phykit:phylogenetic_ordination
pk_pglm = phykit.phykit:phylogenetic_glm
pk_pgls = phykit.phykit:phylogenetic_regression
pk_phenogram = phykit.phykit:phenogram
pk_phmo = phykit.phykit:phylomorphospace
pk_phyl_pca = phykit.phykit:phylogenetic_ordination
pk_phylo_dimreduce = phykit.phykit:phylogenetic_ordination
pk_phylo_glm = phykit.phykit:phylogenetic_glm
pk_phylo_ordination = phykit.phykit:phylogenetic_ordination
pk_phylo_pca = phykit.phykit:phylogenetic_ordination
pk_phylo_regression = phykit.phykit:phylogenetic_regression
pk_phylo_signal = phykit.phykit:phylogenetic_signal
pk_phylogenetic_dimreduce = phykit.phykit:phylogenetic_ordination
pk_phylogenetic_glm = phykit.phykit:phylogenetic_glm
pk_phylogenetic_ordination = phykit.phykit:phylogenetic_ordination
pk_phylogenetic_pca = phykit.phykit:phylogenetic_ordination
pk_phylogenetic_regression = phykit.phykit:phylogenetic_regression
pk_phylogenetic_signal = phykit.phykit:phylogenetic_signal
pk_phylomorpho = phykit.phykit:phylomorphospace
pk_phylomorphospace = phykit.phykit:phylomorphospace
pk_pi = phykit.phykit:pairwise_identity
pk_pis = phykit.phykit:parsimony_informative_sites
pk_plot_alignment_qc = phykit.phykit:plot_alignment_qc
pk_plot_qc = phykit.phykit:plot_alignment_qc
pk_polyt = phykit.phykit:polytomy_test
pk_polyt_test = phykit.phykit:polytomy_test
pk_polytomy_test = phykit.phykit:polytomy_test
pk_ppca = phykit.phykit:phylogenetic_ordination
pk_print = phykit.phykit:print_tree
pk_print_tree = phykit.phykit:print_tree
pk_prune = phykit.phykit:prune_tree
pk_prune_tree = phykit.phykit:prune_tree
pk_ps = phykit.phykit:phylogenetic_signal
pk_pt = phykit.phykit:print_tree
pk_ptt = phykit.phykit:polytomy_test
pk_qnet = phykit.phykit:quartet_network
pk_qpie = phykit.phykit:quartet_pie
pk_quartet_net = phykit.phykit:quartet_network
pk_quartet_network = phykit.phykit:quartet_network
pk_quartet_pie = phykit.phykit:quartet_pie
pk_quartet_pie_chart = phykit.phykit:quartet_pie
pk_rate_heterogeneity = phykit.phykit:rate_heterogeneity
pk_rcv = phykit.phykit:rcv
pk_rcvt = phykit.phykit:rcvt
pk_recode = phykit.phykit:alignment_recoding
pk_rel_comp_var = phykit.phykit:rcv
pk_rel_comp_var_taxon = phykit.phykit:rcvt
pk_relative_composition_variability = phykit.phykit:rcv
pk_relative_composition_variability_taxon = phykit.phykit:rcvt
pk_relative_rate_test = phykit.phykit:relative_rate_test
pk_rename_fasta = phykit.phykit:rename_fasta_entries
pk_rename_fasta_entries = phykit.phykit:rename_fasta_entries
pk_rename_tips = phykit.phykit:rename_tree_tips
pk_rename_tree = phykit.phykit:rename_tree_tips
pk_rename_tree_tips = phykit.phykit:rename_tree_tips
pk_rf = phykit.phykit:rf_distance
pk_rf_dist = phykit.phykit:rf_distance
pk_rf_distance = phykit.phykit:rf_distance
pk_rh = phykit.phykit:rate_heterogeneity
pk_robinson_foulds_distance = phykit.phykit:rf_distance
pk_root = phykit.phykit:root_tree
pk_root_tree = phykit.phykit:root_tree
pk_rrt = phykit.phykit:relative_rate_test
pk_rt = phykit.phykit:root_tree
pk_sat = phykit.phykit:saturation
pk_saturation = phykit.phykit:saturation
pk_scm = phykit.phykit:stochastic_character_map
pk_sd = phykit.phykit:spectral_discordance
pk_simmap = phykit.phykit:stochastic_character_map
pk_sop = phykit.phykit:sum_of_pairs_score
pk_sops = phykit.phykit:sum_of_pairs_score
pk_spec_disc = phykit.phykit:spectral_discordance
pk_spectral_discordance = phykit.phykit:spectral_discordance
pk_splitnet = phykit.phykit:consensus_network
pk_splits_network = phykit.phykit:consensus_network
pk_spurious_seq = phykit.phykit:spurious_sequence
pk_spurious_sequence = phykit.phykit:spurious_sequence
pk_ss = phykit.phykit:spurious_sequence
pk_stochastic_character_map = phykit.phykit:stochastic_character_map
pk_sum_of_pairs_score = phykit.phykit:sum_of_pairs_score
pk_t2t = phykit.phykit:tip_to_tip_distance
pk_t2t_dist = phykit.phykit:tip_to_tip_distance
pk_t2t_nd = phykit.phykit:tip_to_tip_node_distance
pk_t2t_node_dist = phykit.phykit:tip_to_tip_node_distance
pk_tajima_rrt = phykit.phykit:relative_rate_test
pk_tangle = phykit.phykit:cophylo
pk_tanglegram = phykit.phykit:cophylo
pk_tbs = phykit.phykit:terminal_branch_stats
pk_terminal_branch_stats = phykit.phykit:terminal_branch_stats
pk_tg = phykit.phykit:phenogram
pk_thread_dna = phykit.phykit:thread_dna
pk_thresh = phykit.phykit:threshold_model
pk_thresh_bayes = phykit.phykit:threshold_model
pk_threshbayes = phykit.phykit:threshold_model
pk_threshold = phykit.phykit:threshold_model
pk_threshold_model = phykit.phykit:threshold_model
pk_tip_labels = phykit.phykit:tip_labels
pk_tip_to_tip_distance = phykit.phykit:tip_to_tip_distance
pk_tip_to_tip_node_distance = phykit.phykit:tip_to_tip_node_distance
pk_tl = phykit.phykit:tip_labels
pk_tness = phykit.phykit:treeness
pk_tor = phykit.phykit:treeness_over_rcv
pk_total_tree_length = phykit.phykit:total_tree_length
pk_toverr = phykit.phykit:treeness_over_rcv
pk_traitgram = phykit.phykit:phenogram
pk_tree_labels = phykit.phykit:tip_labels
pk_tree_len = phykit.phykit:total_tree_length
pk_treeness = phykit.phykit:treeness
pk_treeness_over_rcv = phykit.phykit:treeness_over_rcv
pk_variable_sites = phykit.phykit:variable_sites
pk_vs = phykit.phykit:variable_sites
