phylogenetic\_inference
=======================

.. currentmodule:: ~hstrat


.. automodule:: hstrat.phylogenetic_inference


   

   
   .. rubric:: Modules

   .. autosummary::
      :toctree:
      :recursive:
   
      ~estimators
      ~pairwise
      ~population
      ~priors
      ~tree
   

   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
      
   
   

   

   .. rubric:: 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.

   .. autosummary::
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
      trie_postprocess
   
   
   

   

   
   
   

   
   
   .. rubric:: Functions

   .. autosummary::
     :toctree:
   
      ~ballpark_patristic_distance_between
      ~ballpark_rank_of_mrca_between
      ~ballpark_ranks_since_mrca_with
      ~build_distance_matrix_biopython
      ~build_distance_matrix_numpy
      ~build_tree
      ~build_tree_nj
      ~build_tree_searchtable
      ~build_tree_trie
      ~build_tree_trie_ensemble
      ~build_tree_upgma
      ~calc_patristic_distance_bounds_between
      ~calc_rank_of_earliest_detectable_mrca_among
      ~calc_rank_of_earliest_detectable_mrca_between
      ~calc_rank_of_mrca_bounds_among
      ~calc_rank_of_mrca_bounds_between
      ~calc_rank_of_mrca_bounds_provided_confidence_level
      ~calc_rank_of_mrca_uncertainty_among
      ~calc_rank_of_mrca_uncertainty_between
      ~calc_ranks_since_earliest_detectable_mrca_with
      ~calc_ranks_since_mrca_bounds_provided_confidence_level
      ~calc_ranks_since_mrca_bounds_with
      ~calc_ranks_since_mrca_uncertainty_with
      ~does_definitively_have_no_common_ancestor
      ~does_definitively_share_no_common_ancestor
      ~does_have_any_common_ancestor
      ~does_share_any_common_ancestor
      ~estimate_patristic_distance_between
      ~estimate_rank_of_mrca_between
      ~estimate_rank_of_mrca_maximum_likelihood
      ~estimate_rank_of_mrca_naive
      ~estimate_rank_of_mrca_unbiased
      ~estimate_ranks_since_mrca_with
   
   

   
   
   .. rubric:: Classes

   .. autosummary::
     :toctree:
   
      ~ArbitraryPrior
      ~AssignDestructionTimeYoungestPlusOneTriePostprocessor
      ~AssignOriginTimeExpectedValueTriePostprocessor
      ~AssignOriginTimeNaiveTriePostprocessor
      ~AssignOriginTimeNodeRankTriePostprocessor
      ~AssignOriginTimeSampleNaiveTriePostprocessor
      ~CompoundTriePostprocessor
      ~ExponentialPrior
      ~GeometricPrior
      ~NopTriePostprocessor
      ~PeelBackConjoinedLeavesTriePostprocessor
      ~SampleAncestralRollbacksTriePostprocessor
      ~UniformPrior