phylogenetic_inference

Tools to infer phylogenetic history from extant genome annotations.

Modules

`estimators`	Tools to estimate MRCA generation from shared ranks of commonality and disparity.
`pairwise`	Functions to infer phylogenetic history between two extant hstrat columns.
`population`	Functions to infer phylogenetic history among a population of extant hstrat columns.
`priors`	Classes to specify prior expectation for the distribution of MRCA generation between hereditary stratigraphic columns, to assist in estimating the phylogenetic relationship of hereditary stratigraphic columns.
`tree`	Functions to reconstruct a phylogenetic tree from extant hereditary strata.

Forwarded Modules

Modules defined elsewhere made available in this namespace for convenience. To view documentation for these modules, use the search bar or navigate to the source package manually.

trie_postprocess

Implementation helpers.

Functions

`ballpark_patristic_distance_between`(first, ...)	Calculate a fast, rough estimate of the patristic distance between first and second.
`ballpark_rank_of_mrca_between`(first, second)	Calculate a fast, rough estimate of the rank of the MRCA beteen first and second.
`ballpark_ranks_since_mrca_with`(focal, other)	Calculate a fast, rough estimate of generations elapsed since MRCA with other.
`build_distance_matrix_biopython`(population, ...)	Compute all-pairs patristic distance among a population of extant hereditary stratigraphic columns as a BioPython DistanceMatrix.
`build_distance_matrix_numpy`(population, ...)	Compute all-pairs patristic distance among a population of extant hereditary stratigraphic columns.
`build_tree`(population, version_pin[, ...])	Estimate the phylogenetic history among hereditary stratigraphic columns.
`build_tree_nj`(population, estimator, prior)	Estimate the phylogenetic history among hereditary stratigraphic columns by using the "unweighted pair group method with neighbor joinint distance-based reconstruction method.
`build_tree_trie`(population[, taxon_labels, ...])	Estimate the phylogenetic history among hereditary stratigraphic columns by building a trie (a.k.a.
`build_tree_trie_ensemble`(population, ...[, ...])	Estimate the phylogenetic history among hereditary stratigraphic columns by building a trie (a.k.a.
`build_tree_upgma`(population, estimator, prior)	Estimate the phylogenetic history among hereditary stratigraphic columns by using the "unweighted pair group method with unweighted means" (UPGMA) distance-based reconstruction method.
`calc_patristic_distance_bounds_between`(...)	What is the total phylogenetic distance along the branch path connecting first and second?
`calc_rank_of_earliest_detectable_mrca_among`(...)	After what generation is common ancstry robustly detectable?
`calc_rank_of_earliest_detectable_mrca_between`(...)	After what generation is common ancstry robustly detectable?
`calc_rank_of_mrca_bounds_among`(population, prior)	Within what generation range did MRCA fall?
`calc_rank_of_mrca_bounds_between`(first, ...)	Within what generation range did MRCA fall?
`calc_rank_of_mrca_bounds_provided_confidence_level`(...)	Calculate provided confidence for a MRCA generation estimate.
`calc_rank_of_mrca_uncertainty_among`(...[, ...])	How wide is the estimate window for generation of MRCA?
`calc_rank_of_mrca_uncertainty_between`(first, ...)	How wide is the estimate window for generation of MRCA?
`calc_ranks_since_earliest_detectable_mrca_with`(...)	How many generations have elapsed since the first where common ancestry with other could be detected?
`calc_ranks_since_mrca_bounds_provided_confidence_level`(...)	Calculate provided confidence for a MRCA generation estimate.
`calc_ranks_since_mrca_bounds_with`(focal, ...)	How many generations have elapsed since MRCA?
`calc_ranks_since_mrca_uncertainty_with`(...)	How wide is the estimation window for generations elapsed since MRCA?
`does_definitively_have_no_common_ancestor`(...)	Does the hereditary stratigraphic record definitively prove that first and second could not possibly share a common ancestor?
`does_definitively_share_no_common_ancestor`(...)	Could the population possibly share a common ancestor?
`does_have_any_common_ancestor`(first, second)	Determine if common ancestry is evidenced with second.
`does_share_any_common_ancestor`(population[, ...])	Determine if common ancestry is evidenced within the population.
`estimate_patristic_distance_between`(first, ...)	Estimate the total phylogenetic distance along the branch path connecting the columns.
`estimate_rank_of_mrca_between`(first, second, ...)	At what generation did the most recent common ancestor of first and second occur?
`estimate_rank_of_mrca_maximum_likelihood`(...)	Estimate the most recent common ancestor (MRCA) at the rank with the highest posterior probability.
`estimate_rank_of_mrca_naive`(...)	Compute a simple, fast estimate the rank of the most recent common ancestor (MRCA).
`estimate_rank_of_mrca_unbiased`(...)	Compute an estimate for the rank of the most recent common ancestor (MRCA) that, on average, avoids systematic over- or under-estimation.
`estimate_ranks_since_mrca_with`(focal, other, ...)	How many generations have elapsed since focal's most recent common ancestor with other?

Classes

`ArbitraryPrior`	Enacts a prior probability density distribution on the generation of the most recent common ancestor (MRCA) between extant hereditary stratigraphic columns that is arbitrary, but computationally efficient.
`AssignDestructionTimeYoungestPlusOneTriePostprocessor`	Functor to assign a destruction time property to trie nodes.
`AssignOriginTimeExpectedValueTriePostprocessor`	Functor to assign origin time property to trie nodes using expected values over the distribution of possible differentia collisions.
`AssignOriginTimeNaiveTriePostprocessor`	Functor to assign origin time property to trie nodes calculated as the average of the node's rank and the minimum rank among its children.
`AssignOriginTimeNodeRankTriePostprocessor`	Functor to assign trie nodes' rank as their the origin time.
`AssignOriginTimeSampleNaiveTriePostprocessor`	Functor to assign origin time property to trie nodes sampled between the node's rank and the minimum rank among its children.
`CompoundTriePostprocessor`	Functor to sequentially apply multiple trie postprocessors.
`ExponentialPrior`	Enacts a prior expectation that the generation of the most recent common ancestor (MRCA) between extant hereditary stratigraphic columns becomes exponentialy less likely with increasing antiquity.
`GeometricPrior`	Enacts a prior expectation that the generation of the most recent common ancestor (MRCA) between extant hereditary stratigraphic columns becomes exponentialy less likely with increasing antiquity.
`PeelBackConjoinedLeavesTriePostprocessor`	Functor to separate any TrieLeafNode instances that are direct siblings.
`SampleAncestralRollbacksTriePostprocessor`	Functor to correct for systematic overestimation of relatedness by sampling a compensatory adjustment to trie topology.
`UniformPrior`	Enacts a prior expectation that the generation of the most recent common ancestor (MRCA) is equally likely to occur at any generation since genesis.