Man pages for castor
Efficient Phylogenetics on Large Trees

asr_empirical_probabilitiesEmpirical ancestral state probabilities.
asr_independent_contrastsAncestral state reconstruction via phylogenetic independent...
asr_max_parsimonyMaximum-parsimony ancestral state reconstruction.
asr_mk_modelAncestral state reconstruction with Mk models and rerooting
asr_squared_change_parsimonySquared-change parsimony ancestral state reconstruction.
asr_subtree_averagingAncestral state reconstruction via subtree averaging.
castorEfficient computations on large phylogenetic trees.
collapse_monofurcationsRemove monofurcations from a tree.
collapse_tree_at_resolutionCollapse nodes of a tree at a phylogenetic resolution.
congruent_divergence_timesExtract dating anchors for a target tree, using a dated...
congruent_hbds_modelGenerate a congruent homogenous-birth-death-sampling model.
count_lineages_through_timeCount number of lineages through time (LTT).
count_tips_per_nodeCount descending tips.
count_transitions_between_cladesCount the number of state transitions between tips or nodes.
date_tree_redDate a tree based on relative evolutionary divergences.
evaluate_splineEvaluate a scalar spline at arbitrary locations.
exponentiate_matrixExponentiate a matrix.
extend_tree_to_heightExtend a rooted tree up to a specific height.
extract_fasttree_constraintsExtract tree constraints in FastTree alignment format.
find_farthest_tip_pairFind the two most distant tips in a tree.
find_farthest_tipsFind farthest tip to each tip & node of a tree.
find_nearest_tipsFind nearest tip to each tip & node of a tree.
find_rootFind the root of a tree.
find_root_of_monophyletic_tipsFind the node or tip that, as root, would make a set of...
fit_and_compare_bm_modelsFit and compare Brownian Motion models for multivariate trait...
fit_and_compare_sbm_constFit and compare Spherical Brownian Motion models for...
fit_bm_modelFit a Brownian Motion model for multivariate trait evolution.
fit_hbd_model_on_gridFit a homogenous birth-death model on a discrete time grid.
fit_hbd_model_parametricFit a parametric homogenous birth-death model to a timetree.
fit_hbd_pdr_on_gridFit pulled diversification rates of birth-death models on a...
fit_hbd_pdr_parametricFit parameterized pulled diversification rates of birth-death...
fit_hbd_psr_on_gridFit pulled speciation rates of birth-death models on a time...
fit_hbds_model_on_gridFit a homogenous birth-death-sampling model on a discrete...
fit_hbds_model_parametricFit a parametric homogenous birth-death-sampling model to a...
fit_mkFit a Markov (Mk) model for discrete trait evolution.
fit_musseFit a discrete-state-dependent diversification model via...
fit_sbm_constFit a phylogeographic Spherical Brownian Motion model.
fit_sbm_geobiased_constFit a phylogeographic Spherical Brownian Motion model with...
fit_sbm_linearFit a phylogeographic Spherical Brownian Motion model with...
fit_sbm_on_gridFit a phylogeographic Spherical Brownian Motion model with...
fit_sbm_parametricFit a time-dependent phylogeographic Spherical Brownian...
fit_tree_modelFit a cladogenic model to an existing tree.
gamma_statisticCalculate the gamma-statistic of a tree.
generate_gene_tree_mscGenerate a gene tree based on the multi-species coalescent...
generate_gene_tree_msc_hgt_dlGenerate gene trees based on the multi-species coalescent,...
generate_random_treeGenerate a tree using a Poissonian speciation/extinction...
generate_tree_hbd_reverseGenerate a tree from a birth-death model in reverse time.
generate_tree_hbdsGenerate a tree from a birth-death-sampling model in forward...
generate_tree_with_evolving_ratesGenerate a random tree with evolving speciation/extinction...
geographic_acfPhylogenetic autocorrelation function of geographic...
get_all_distances_to_rootGet distances of all tips and nodes to the root.
get_all_node_depthsGet the phylogenetic depth of each node in a tree.
get_all_pairwise_distancesGet distances between all pairs of tips and/or nodes.
get_clade_listGet a representation of a tree as a table listing tips/nodes.
get_independent_contrastsPhylogenetic independent contrasts for continuous traits.
get_mrca_of_setMost recent common ancestor of a set of tips/nodes.
get_pairwise_distancesGet distances between pairs of tips or nodes.
get_pairwise_mrcasGet most recent common ancestors of tip/node pairs.
get_random_diffusivity_matrixCreate a random diffusivity matrix for a Brownian motion...
get_random_mk_transition_matrixCreate a random transition matrix for an Mk model.
get_redsCalculate relative evolutionary divergences in a tree.
get_stationary_distributionStationary distribution of Markov transition matrix.
get_subtree_at_nodeExtract a subtree descending from a specific node.
get_subtrees_at_nodesExtract subtrees descending from specific nodes.
get_subtree_with_tipsExtract a subtree spanning a specific subset of tips.
get_tips_for_mrcasFind tips with specific most recent common ancestors.
get_trait_acfPhylogenetic autocorrelation function of a numeric trait.
get_trait_depthCalculate depth of phylogenetic conservatism for a binary...
get_trait_stats_over_timeCalculate mean & standard deviation of a numeric trait on a...
get_transition_index_matrixCreate an index matrix for a Markov transition model.
get_tree_spanGet min and max distance of any tip to the root.
get_tree_traversal_root_to_tipsTraverse tree from root to tips.
hsp_binomialHidden state prediction for a binary trait based on the...
hsp_empirical_probabilitiesHidden state prediction via empirical probabilities.
hsp_independent_contrastsHidden state prediction via phylogenetic independent...
hsp_max_parsimonyHidden state prediction via maximum parsimony.
hsp_mk_modelHidden state prediction with Mk models and rerooting
hsp_nearest_neighborHidden state prediction based on nearest neighbor.
hsp_squared_change_parsimonyHidden state prediction via squared-change parsimony.
hsp_subtree_averagingHidden state prediction via subtree averaging.
is_monophyleticDetermine if a set of tips is monophyletic.
join_rooted_treesJoin two rooted trees.
loglikelihood_hbdGalculate the log-likelihood of a homogenous birth-death...
map_to_state_spaceMap states of a discrete trait to integers.
merge_nodes_to_multifurcationsMerge specific nodes into multifurcations.
merge_short_edgesEliminate short edges in a tree by merging nodes into...
model_adequacy_hbdCheck if a birth-death model adequately explains a timetree.
model_adequacy_hbdsCheck if a birth-death-sampling model adequately explains a...
multifurcations_to_bifurcationsExpand multifurcations to bifurcations.
pick_random_tipsPick random subsets of tips on a tree.
read_treeLoad a tree from a string or file in Newick (parenthetic)...
reconstruct_past_diversificationReconstruct past diversification dynamics from a diversity...
reorder_tree_edgesReorder tree edges in preorder or postorder.
root_at_midpointRoot or re-root a tree at the midpoint node.
root_at_nodeRoot or re-root a tree at a specific node.
root_in_edgeRoot or re-root a tree in the middle of an edge.
root_via_outgroupRoot or re-root a tree based on an outgroup tip.
shift_clade_timesShift the time of specific nodes & tips.
simulate_bm_modelSimulate a Brownian motion model for multivariate trait...
simulate_deterministic_hbdSimulate a deterministic homogenous birth-death model.
simulate_deterministic_hbdsSimulate a deterministic homogenous birth-death-sampling...
simulate_diversification_modelSimulate a deterministic uniform speciation/extinction model.
simulate_dsseSimulate a Discrete-State Speciation and Extinction (dSSE)...
simulate_mk_modelSimulate an Mk model for discrete trait evolution.
simulate_ou_modelSimulate an Ornstein-Uhlenbeck model for continuous trait...
simulate_rou_modelSimulate a reflected Ornstein-Uhlenbeck model for continuous...
simulate_sbmSimulate Spherical Brownian Motion on a tree.
simulate_tdsseSimulate a time-dependent Discrete-State Speciation and...
split_tree_at_heightSplit a tree into subtrees at a specific height.
tree_distanceCalculate the distance between two trees.
tree_from_branching_agesGenerate a random timetree with specific branching ages.
tree_from_sampling_branching_agesGenerate a random timetree with specific tip/sampling and...
tree_imbalanceCalculate various imbalance statistics for a tree.
trim_tree_at_heightTrim a rooted tree down to a specific height.
write_treeWrite a tree in Newick (parenthetic) format.
castor documentation built on June 21, 2021, 1:06 a.m.