test_drive

Tools to create phylogenies and corresponding extant populations of hereditary stratigraph columns.

Modules

generate_template_phylogeny	Tools to generate example phylogenies.
perfect_tracking	Tools for perfect phylogenetic tracking.

Functions

compile_perfect_backtrack_phylogeny(population)	Compile phylogenetic history tracked using PerfectBacktrackHandle breadcrumbs.
compile_phylogeny_from_lineage_iters(population)	Compile phylogenetic history tracked using generic backtracking breadcrumbs.
descend_template_phylogeny(...[, demark, ...])	Generate a population of hereditary stratigraphic columns that could have resulted from the template phylogeny.
descend_template_phylogeny_alifestd(...[, ...])	Generate a population of hereditary stratigraphic columns that could have resulted from the template phylogeny.
descend_template_phylogeny_biopython(tree, ...)	Generate a population of hereditary stratigraphic columns that could have resulted from the template phylogeny.
descend_template_phylogeny_dendropy(tree, ...)	Generate a population of hereditary stratigraphic columns that could have resulted from the template phylogeny.
descend_template_phylogeny_naive(...[, ...])	Generate a population of hereditary stratigraphic columns that could have resulted from the template phylogeny.
descend_template_phylogeny_networkx(tree, ...)	Generate a population of hereditary stratigraphic columns that could have resulted from the template phylogeny.
descend_template_phylogeny_posthoc(...[, ...])	Generate a population of hereditary stratigraphic columns that could have resulted from the template phylogeny.
evolve_fitness_trait_population([...])	Run simple evolutionary simulation to generate sample phylogeny.
iter_perfect_backtrack_lineage(handle)	Iterate up PerfectBacktrackHandle breadcrumbs for line of descent ending in handle, including handle.

Classes

DecantingPhyloTracker	Data structure to enable perfect tracking over a fixed-size population with synchronous generations.
GarbageCollectingPhyloTracker	Data structure to enable perfect tracking over a fixed-size population with synchronous generations.
PerfectBacktrackHandle	Breadcrumb for perfectly backtracking a phylogenetic chain of descent.