asr_empirical_probabilities
                        Empirical ancestral state probabilities.
asr_independent_contrasts
                        Ancestral state reconstruction via phylogenetic
                        independent contrasts.
asr_max_parsimony       Maximum-parsimony ancestral state
                        reconstruction.
asr_mk_model            Ancestral state reconstruction with Mk models
                        and rerooting
asr_squared_change_parsimony
                        Squared-change parsimony ancestral state
                        reconstruction.
asr_subtree_averaging   Ancestral state reconstruction via subtree
                        averaging.
castor-package          Efficient computations on large phylogenetic
                        trees.
clade_densities         Estimate the density of tips & nodes in a
                        timetree.
collapse_monofurcations
                        Remove monofurcations from a tree.
collapse_tree_at_resolution
                        Collapse nodes of a tree at a phylogenetic
                        resolution.
congruent_divergence_times
                        Extract dating anchors for a target tree, using
                        a dated reference tree
congruent_hbds_model    Generate a congruent
                        homogenous-birth-death-sampling model.
consensus_taxonomies    Compute consensus taxonomies across a tree.
consentrait_depth       Calculate phylogenetic depth of a binary trait
                        using the consenTRAIT metric.
correlate_discrete_traits
                        Correlations between discrete traits on trees.
correlate_phylo_geodistances
                        Correlations between phylogenetic & geographic
                        distances.
count_lineages_through_time
                        Count number of lineages through time (LTT).
count_tips_per_node     Count descending tips.
count_transitions_between_clades
                        Count the number of state transitions between
                        tips or nodes.
date_tree_red           Date a tree based on relative evolutionary
                        divergences.
discrete_trait_depth    Calculate phylogenetic depth of a discrete
                        trait.
evaluate_spline         Evaluate a scalar spline at arbitrary
                        locations.
expanded_tree_from_jplace
                        Place queries on a tree from a jplace file.
expected_distances_sbm
                        Expected distances traversed by a Spherical
                        Brownian Motion.
exponentiate_matrix     Exponentiate a matrix.
extend_tree_to_height   Extend a rooted tree up to a specific height.
extract_deep_frame      Extract tips representing a tree's deep splits.
extract_fasttree_constraints
                        Extract tree constraints in FastTree alignment
                        format.
extract_tip_neighborhood
                        Extract a subtree spanning tips within a
                        certain neighborhood.
extract_tip_radius      Extract a subtree spanning tips within a
                        certain radius.
find_farthest_tip_pair
                        Find the two most distant tips in a tree.
find_farthest_tips      Find farthest tip to each tip & node of a tree.
find_nearest_tips       Find nearest tip to each tip & node of a tree.
find_root               Find the root of a tree.
find_root_of_monophyletic_tips
                        Find the node or tip that, as root, would make
                        a set of target tips monophyletic.
fit_and_compare_bm_models
                        Fit and compare Brownian Motion models for
                        multivariate trait evolution between two data
                        sets.
fit_and_compare_sbm_const
                        Fit and compare Spherical Brownian Motion
                        models for diffusive geographic dispersal
                        between two data sets.
fit_bm_model            Fit a Brownian Motion model for multivariate
                        trait evolution.
fit_hbd_model_on_grid   Fit a homogenous birth-death model on a
                        discrete time grid.
fit_hbd_model_parametric
                        Fit a parametric homogenous birth-death model
                        to a timetree.
fit_hbd_pdr_on_best_grid_size
                        Fit pulled diversification rates of birth-death
                        models on a time grid with optimal size.
fit_hbd_pdr_on_grid     Fit pulled diversification rates of birth-death
                        models on a time grid.
fit_hbd_pdr_parametric
                        Fit parameterized pulled diversification rates
                        of birth-death models.
fit_hbd_psr_on_best_grid_size
                        Fit pulled speciation rates of birth-death
                        models on a time grid with optimal size.
fit_hbd_psr_on_grid     Fit pulled speciation rates of birth-death
                        models on a time grid.
fit_hbd_psr_parametric
                        Fit parameterized pulled speciation rates of
                        birth-death models.
fit_hbds_model_on_grid
                        Fit a homogenous birth-death-sampling model on
                        a discrete time grid.
fit_hbds_model_parametric
                        Fit a parametric homogenous
                        birth-death-sampling model to a timetree.
fit_mk                  Fit a Markov (Mk) model for discrete trait
                        evolution.
fit_musse               Fit a discrete-state-dependent diversification
                        model via maximum-likelihood.
fit_sbm_const           Fit a phylogeographic Spherical Brownian Motion
                        model.
fit_sbm_geobiased_const
                        Fit a phylogeographic Spherical Brownian Motion
                        model with geographic sampling bias.
fit_sbm_linear          Fit a phylogeographic Spherical Brownian Motion
                        model with linearly varying diffusivity.
fit_sbm_on_grid         Fit a phylogeographic Spherical Brownian Motion
                        model with piecewise-linear diffusivity.
fit_sbm_parametric      Fit a time-dependent phylogeographic Spherical
                        Brownian Motion model.
fit_tree_model          Fit a cladogenic model to an existing tree.
gamma_statistic         Calculate the gamma-statistic of a tree.
generate_gene_tree_msc
                        Generate a gene tree based on the multi-species
                        coalescent model.
generate_gene_tree_msc_hgt_dl
                        Generate gene trees based on the multi-species
                        coalescent, horizontal gene transfers and
                        duplications/losses.
generate_random_tree    Generate a tree using a Poissonian
                        speciation/extinction model.
generate_tree_hbd_reverse
                        Generate a tree from a birth-death model in
                        reverse time.
generate_tree_hbds      Generate a tree from a birth-death-sampling
                        model in forward time.
generate_tree_with_evolving_rates
                        Generate a random tree with evolving
                        speciation/extinction rates.
geographic_acf          Phylogenetic autocorrelation function of
                        geographic locations.
get_all_distances_to_root
                        Get distances of all tips and nodes to the
                        root.
get_all_distances_to_tip
                        Get distances of all tips/nodes to a focal tip.
get_all_node_depths     Get the phylogenetic depth of each node in a
                        tree.
get_all_pairwise_distances
                        Get distances between all pairs of tips and/or
                        nodes.
get_ancestral_nodes     Compute ancestral nodes.
get_clade_list          Get a representation of a tree as a table
                        listing tips/nodes.
get_independent_contrasts
                        Phylogenetic independent contrasts for
                        continuous traits.
get_independent_sister_tips
                        Extract disjoint tip pairs with independent
                        relationships.
get_mrca_of_set         Most recent common ancestor of a set of
                        tips/nodes.
get_pairwise_distances
                        Get distances between pairs of tips or nodes.
get_pairwise_mrcas      Get most recent common ancestors of tip/node
                        pairs.
get_random_diffusivity_matrix
                        Create a random diffusivity matrix for a
                        Brownian motion model.
get_random_mk_transition_matrix
                        Create a random transition matrix for an Mk
                        model.
get_reds                Calculate relative evolutionary divergences in
                        a tree.
get_stationary_distribution
                        Stationary distribution of Markov transition
                        matrix.
get_subtree_at_node     Extract a subtree descending from a specific
                        node.
get_subtree_with_tips   Extract a subtree spanning a specific subset of
                        tips.
get_subtrees_at_nodes   Extract subtrees descending from specific
                        nodes.
get_tips_for_mrcas      Find tips with specific most recent common
                        ancestors.
get_trait_acf           Phylogenetic autocorrelation function of a
                        numeric trait.
get_trait_stats_over_time
                        Calculate mean & standard deviation of a
                        numeric trait on a dated tree over time.
get_transition_index_matrix
                        Create an index matrix for a Markov transition
                        model.
get_tree_span           Get min and max distance of any tip to the
                        root.
get_tree_traversal_root_to_tips
                        Traverse tree from root to tips.
hsp_binomial            Hidden state prediction for a binary trait
                        based on the binomial distribution.
hsp_empirical_probabilities
                        Hidden state prediction via empirical
                        probabilities.
hsp_independent_contrasts
                        Hidden state prediction via phylogenetic
                        independent contrasts.
hsp_max_parsimony       Hidden state prediction via maximum parsimony.
hsp_mk_model            Hidden state prediction with Mk models and
                        rerooting
hsp_naive               Naive hidden state prediction.
hsp_nearest_neighbor    Hidden state prediction based on nearest
                        neighbor.
hsp_squared_change_parsimony
                        Hidden state prediction via squared-change
                        parsimony.
hsp_subtree_averaging   Hidden state prediction via subtree averaging.
inherit_taxonomies      Inherit ancestral taxonomies from a phylogeny.
is_bifurcating          Determine if a tree is bifurcating.
is_monophyletic         Determine if a set of tips is monophyletic.
join_rooted_trees       Join two rooted trees.
loglikelihood_hbd       Galculate the log-likelihood of a homogenous
                        birth-death model.
map_to_state_space      Map states of a discrete trait to integers.
mean_abs_change_scalar_ou
                        Compute the expected absolute change of an
                        Ornstein-Uhlenbeck process.
merge_nodes_to_multifurcations
                        Merge specific nodes into multifurcations.
merge_short_edges       Eliminate short edges in a tree by merging
                        nodes into multifurcations.
model_adequacy_hbd      Check if a birth-death model adequately
                        explains a timetree.
model_adequacy_hbds     Check if a birth-death-sampling model
                        adequately explains a timetree.
multifurcations_to_bifurcations
                        Expand multifurcations to bifurcations.
pick_random_tips        Pick random subsets of tips on a tree.
place_tips_taxonomically
                        Place queries on a tree based on taxonomic
                        identities.
plot_tree_radial        Plot a tree in radial layout.
read_fasta              Load a fasta file.
read_fastq              Load a fastq file.
read_tree               Load a tree from a string or file in Newick
                        (parenthetic) format.
reconstruct_past_diversification
                        Reconstruct past diversification dynamics from
                        a diversity time series.
reorder_tree_edges      Reorder tree edges in preorder or postorder.
root_at_midpoint        Root a tree at the midpoint node.
root_at_node            Root a tree at a specific node.
root_in_edge            Root a tree in the middle of an edge.
root_via_outgroup       Root a tree based on an outgroup tip.
root_via_rtt            Root a tree via root-to-tip regression.
shift_clade_times       Shift the time of specific nodes & tips.
simulate_bm_model       Simulate a Brownian motion model for
                        multivariate trait co-evolution.
simulate_deterministic_hbd
                        Simulate a deterministic homogenous birth-death
                        model.
simulate_deterministic_hbds
                        Simulate a deterministic homogenous
                        birth-death-sampling model.
simulate_diversification_model
                        Simulate a deterministic uniform
                        speciation/extinction model.
simulate_dsse           Simulate a Discrete-State Speciation and
                        Extinction (dSSE) model.
simulate_mk_model       Simulate an Mk model for discrete trait
                        evolution.
simulate_ou_model       Simulate an Ornstein-Uhlenbeck model for
                        continuous trait evolution.
simulate_rou_model      Simulate a reflected Ornstein-Uhlenbeck model
                        for continuous trait evolution.
simulate_sbm            Simulate Spherical Brownian Motion on a tree.
simulate_tdsse          Simulate a time-dependent Discrete-State
                        Speciation and Extinction (tdSSE) model.
spline_coefficients     Get the polynomial coefficients of a spline.
split_tree_at_height    Split a tree into subtrees at a specific
                        height.
tree_distance           Calculate the distance between two trees.
tree_from_branching_ages
                        Generate a random timetree with specific
                        branching ages.
tree_from_sampling_branching_ages
                        Generate a random timetree with specific
                        tip/sampling and node/branching ages.
tree_from_taxa          Construct a rooted tree from lists of taxa.
tree_imbalance          Calculate various imbalance statistics for a
                        tree.
trim_tree_at_height     Trim a rooted tree down to a specific height.
write_tree              Write a tree in Newick (parenthetic) format.
