Efficient Phylogenetics on Large Trees

asr_empirical_probabilities | Empirical ancestral state probabilities. |

asr_independent_contrasts | Ancestral state reconstruction via phylogenetic independent... |

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 | 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... |

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... |

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... |

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... |

fit_and_compare_bm_models | Fit and compare Brownian Motion models for multivariate trait... |

fit_and_compare_sbm_const | Fit and compare Spherical Brownian Motion models for... |

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... |

fit_hbd_pdr_on_grid | Fit pulled diversification rates of birth-death models on a... |

fit_hbd_pdr_parametric | Fit parameterized pulled diversification rates of birth-death... |

fit_hbd_psr_on_best_grid_size | Fit pulled speciation rates of birth-death models on a time... |

fit_hbd_psr_on_grid | Fit pulled speciation rates of birth-death models on a time... |

fit_hbd_psr_parametric | Fit parameterized pulled speciation rates of birth-death... |

fit_hbds_model_on_grid | Fit a homogenous birth-death-sampling model on a discrete... |

fit_hbds_model_parametric | Fit a parametric homogenous birth-death-sampling model to a... |

fit_mk | Fit a Markov (Mk) model for discrete trait evolution. |

fit_musse | Fit a discrete-state-dependent diversification model via... |

fit_sbm_const | Fit a phylogeographic Spherical Brownian Motion model. |

fit_sbm_geobiased_const | Fit a phylogeographic Spherical Brownian Motion model with... |

fit_sbm_linear | Fit a phylogeographic Spherical Brownian Motion model with... |

fit_sbm_on_grid | Fit a phylogeographic Spherical Brownian Motion model with... |

fit_sbm_parametric | Fit a time-dependent phylogeographic Spherical Brownian... |

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... |

generate_gene_tree_msc_hgt_dl | Generate gene trees based on the multi-species coalescent,... |

generate_random_tree | Generate a tree using a Poissonian speciation/extinction... |

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... |

generate_tree_with_evolving_rates | Generate a random tree with evolving speciation/extinction... |

geographic_acf | Phylogenetic autocorrelation function of geographic... |

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... |

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_subtrees_at_nodes | Extract subtrees descending from specific nodes. |

get_subtree_with_tips | Extract a subtree spanning a specific subset of tips. |

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... |

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... |

hsp_empirical_probabilities | Hidden state prediction via empirical probabilities. |

hsp_independent_contrasts | Hidden state prediction via phylogenetic independent... |

hsp_max_parsimony | Hidden state prediction via maximum parsimony. |

hsp_mk_model | Hidden state prediction with Mk models and rerooting |

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. |

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... |

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... |

merge_nodes_to_multifurcations | Merge specific nodes into multifurcations. |

merge_short_edges | Eliminate short edges in a tree by merging nodes into... |

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... |

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. |

read_tree | Load a tree from a string or file in Newick (parenthetic)... |

reconstruct_past_diversification | Reconstruct past diversification dynamics from a diversity... |

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... |

simulate_deterministic_hbd | Simulate a deterministic homogenous birth-death model. |

simulate_deterministic_hbds | Simulate a deterministic homogenous birth-death-sampling... |

simulate_diversification_model | Simulate a deterministic uniform speciation/extinction model. |

simulate_dsse | Simulate a Discrete-State Speciation and Extinction (dSSE)... |

simulate_mk_model | Simulate an Mk model for discrete trait evolution. |

simulate_ou_model | Simulate an Ornstein-Uhlenbeck model for continuous trait... |

simulate_rou_model | Simulate a reflected Ornstein-Uhlenbeck model for continuous... |

simulate_sbm | Simulate Spherical Brownian Motion on a tree. |

simulate_tdsse | Simulate a time-dependent Discrete-State Speciation and... |

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... |

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. |

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