Tools

This library stores code for post-reconstruction analysis of trees. We are always in the process of developing new statistics and tools for helping us interpret trees, and adding them to this library.

Autocorrelation

tl.compute_morans_i(tree[, meta_columns, X, ...])

Computes Moran's I statistic.

Branch Length Estimation (BLE)

tl.IIDExponentialBayesian(mutation_rate, ...)	Inference under a subsampled Birth Process with IID memoryless mutations.
tl.IIDExponentialMLE([...])	MLE under a model of IID memoryless CRISPR/Cas9 mutations.

Coupling

tl.compute_evolutionary_coupling(tree, ...)

Computes Evolutionary Coupling of categorical variables.

Metrics

tl.calculate_likelihood_continuous(tree[, ...])	Calculates the log likelihood of a tree under a continuous process.
tl.calculate_likelihood_discrete(tree[, ...])	Calculates the log likelihood of a tree under a discrete process.
tl.calculate_parsimony(tree[, ...])	Calculates the number of mutations that have occurred on a tree.

Parameter Estimation

tl.estimate_missing_data_rates(tree[, ...])	Estimates both missing data parameters given one of the two from a tree.
tl.estimate_mutation_rate(tree[, ...])	Estimates the mutation rate from a tree and character matrix.

Small-Parsimony

tl.fitch_count(cassiopeia_tree, meta_item[, ...])	Runs the FitchCount algorithm.
tl.fitch_hartigan(cassiopeia_tree, meta_item)	Run the Fitch-Hartigan algorithm.
tl.score_small_parsimony(cassiopeia_tree, ...)	Computes the small-parsimony of the tree.

Topology

tl.compute_expansion_pvalues(tree[, ...])

Call expansion pvalues on a tree.