phylotrackpy
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Phylotrackpy Documentation
Introduction
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Position based tracking
Example Usage
Nuances of Exact Phylogenies
Glossary
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phylotrackpy
Index
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Index
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A
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B
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C
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G
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I
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L
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M
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N
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O
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P
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R
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S
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T
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U
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W
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__init__() (phylotrackpy.systematics.Systematics method)
(phylotrackpy.systematics.Taxon method)
(phylotrackpy.systematics.WorldPosition method)
A
add_org() (phylotrackpy.systematics.Systematics method)
add_org_by_position() (phylotrackpy.systematics.Systematics method)
add_snapshot_fun() (phylotrackpy.systematics.Systematics method)
B
Bifurcation
C
calc_diversity() (phylotrackpy.systematics.Systematics method)
Coalescence events
colless_like_index() (phylotrackpy.systematics.Systematics method)
G
get_active_taxa() (phylotrackpy.systematics.Systematics method)
get_active_taxa_reference() (phylotrackpy.systematics.Systematics method)
get_ancestor_taxa() (phylotrackpy.systematics.Systematics method)
get_ave_depth() (phylotrackpy.systematics.Systematics method)
get_average_origin_time() (phylotrackpy.systematics.Systematics method)
get_branches_to_root() (phylotrackpy.systematics.Systematics method)
get_destruction_time() (phylotrackpy.systematics.Taxon method)
get_distance_to_root() (phylotrackpy.systematics.Systematics method)
get_id() (phylotrackpy.systematics.Taxon method)
get_index() (phylotrackpy.systematics.WorldPosition method)
get_info() (phylotrackpy.systematics.Taxon method)
get_max_depth() (phylotrackpy.systematics.Systematics method)
get_mean_evolutionary_distinctiveness() (phylotrackpy.systematics.Systematics method)
get_mean_pairwise_distance() (phylotrackpy.systematics.Systematics method)
get_most_recent() (phylotrackpy.systematics.Systematics method)
get_mrca() (phylotrackpy.systematics.Systematics method)
get_next_id() (phylotrackpy.systematics.Systematics method)
get_next_parent() (phylotrackpy.systematics.Systematics method)
get_num_active() (phylotrackpy.systematics.Systematics method)
get_num_ancestors() (phylotrackpy.systematics.Systematics method)
get_num_offspring() (phylotrackpy.systematics.Taxon method)
get_num_orgs() (phylotrackpy.systematics.Taxon method)
get_num_outside() (phylotrackpy.systematics.Systematics method)
get_num_roots() (phylotrackpy.systematics.Systematics method)
get_num_taxa() (phylotrackpy.systematics.Systematics method)
get_offspring() (phylotrackpy.systematics.Taxon method)
get_origination_time() (phylotrackpy.systematics.Taxon method)
get_out_degree_distribution() (phylotrackpy.systematics.Systematics method)
get_outside_taxa() (phylotrackpy.systematics.Systematics method)
get_pairwise_distance() (phylotrackpy.systematics.Systematics method)
get_pairwise_distances() (phylotrackpy.systematics.Systematics method)
get_parent() (phylotrackpy.systematics.Taxon method)
get_phylogenetic_diversity() (phylotrackpy.systematics.Systematics method)
get_pop_ID() (phylotrackpy.systematics.WorldPosition method)
get_shared_ancestor() (phylotrackpy.systematics.Systematics method)
get_store_active() (phylotrackpy.systematics.Systematics method)
get_store_ancestors() (phylotrackpy.systematics.Systematics method)
get_store_archive() (phylotrackpy.systematics.Systematics method)
get_store_outside() (phylotrackpy.systematics.Systematics method)
get_store_position() (phylotrackpy.systematics.Systematics method)
get_sum_distance() (phylotrackpy.systematics.Systematics method)
get_sum_evolutionary_distinctiveness() (phylotrackpy.systematics.Systematics method)
get_sum_pairwise_distance() (phylotrackpy.systematics.Systematics method)
get_taxon_at() (phylotrackpy.systematics.Systematics method)
get_total_offspring() (phylotrackpy.systematics.Taxon method)
get_total_orgs() (phylotrackpy.systematics.Systematics method)
(phylotrackpy.systematics.Taxon method)
get_track_synchronous() (phylotrackpy.systematics.Systematics method)
get_tree_size() (phylotrackpy.systematics.Systematics method)
get_update() (phylotrackpy.systematics.Systematics method)
get_variance_evolutionary_distinctiveness() (phylotrackpy.systematics.Systematics method)
get_variance_pairwise_distance() (phylotrackpy.systematics.Systematics method)
I
is_active() (phylotrackpy.systematics.WorldPosition method)
is_taxon_at() (phylotrackpy.systematics.Systematics method)
is_valid() (phylotrackpy.systematics.WorldPosition method)
L
Leaf node
load_from_file() (phylotrackpy.systematics.Systematics method)
M
module
phylotrackpy.systematics
Most Recent Common Ancestor (MRCA)
mrca_depth() (phylotrackpy.systematics.Systematics method)
Multifurcation
N
Non-branch node
O
on_extinct() (phylotrackpy.systematics.Systematics method)
on_new() (phylotrackpy.systematics.Systematics method)
on_prune() (phylotrackpy.systematics.Systematics method)
P
parent() (phylotrackpy.systematics.Systematics method)
phylotrackpy.systematics
module
Polytomy
print_lineage() (phylotrackpy.systematics.Systematics method)
print_status() (phylotrackpy.systematics.Systematics method)
R
remove_before() (phylotrackpy.systematics.Systematics method)
remove_org() (phylotrackpy.systematics.Systematics method)
remove_org_after_repro() (phylotrackpy.systematics.Systematics method)
remove_org_by_position() (phylotrackpy.systematics.Systematics method)
remove_org_by_position_after_repro() (phylotrackpy.systematics.Systematics method)
S
sackin_index() (phylotrackpy.systematics.Systematics method)
set_calc_info_fun() (phylotrackpy.systematics.Systematics method)
set_next_parent() (phylotrackpy.systematics.Systematics method)
set_next_parent_by_position() (phylotrackpy.systematics.Systematics method)
set_store_active() (phylotrackpy.systematics.Systematics method)
set_store_ancestors() (phylotrackpy.systematics.Systematics method)
set_store_archive() (phylotrackpy.systematics.Systematics method)
set_store_outside() (phylotrackpy.systematics.Systematics method)
set_store_position() (phylotrackpy.systematics.Systematics method)
set_track_synchronous() (phylotrackpy.systematics.Systematics method)
set_update() (phylotrackpy.systematics.Systematics method)
snapshot() (phylotrackpy.systematics.Systematics method)
swap_positions() (phylotrackpy.systematics.Systematics method)
Systematics (class in phylotrackpy.systematics)
T
Taxa
Taxon
(class in phylotrackpy.systematics)
U
update() (phylotrackpy.systematics.Systematics method)
W
WorldPosition (class in phylotrackpy.systematics)
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