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Title: ARGs as tree sequences — Tree Sequence Tutorials

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Domain: tskit.dev

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Links:

Skip to main contenthttps://tskit.dev/tutorials/args.html#main-content
https://tskit.dev/tutorials/intro.html
What is a tree sequence?https://tskit.dev/tutorials/what_is.html
Terminology & conceptshttps://tskit.dev/tutorials/terminology_and_concepts.html
Getting started with tskithttps://tskit.dev/tutorials/getting_started.html
Analysing tree sequenceshttps://tskit.dev/tutorials/analysing_tree_sequences.html
Analysing treeshttps://tskit.dev/tutorials/analysing_trees.html
Incremental algorithmshttps://tskit.dev/tutorials/incremental_algorithms.html
Counting topologieshttps://tskit.dev/tutorials/counting_topologies.html
Parallelizationhttps://tskit.dev/tutorials/parallelization.html
PCA, on branches and SNPshttps://tskit.dev/tutorials/PCA.html
Tables and editinghttps://tskit.dev/tutorials/tables_and_editing.html
Simplificationhttps://tskit.dev/tutorials/simplification.html
Advanced simplificationhttps://tskit.dev/tutorials/advanced_simplification.html
Visualizationhttps://tskit.dev/tutorials/viz.html
Working with Metadatahttps://tskit.dev/tutorials/metadata.html
ARGs as tree sequenceshttps://tskit.dev/tutorials/args.html
Tree sequences and simulationhttps://tskit.dev/tutorials/simulation_overview.html
Do you really need mutations?https://tskit.dev/tutorials/no_mutations.html
Advanced msprime topicshttps://tskit.dev/tutorials/advanced_msprime.html
Demographyhttps://tskit.dev/tutorials/demography.html
Instantaneous Bottleneckshttps://tskit.dev/tutorials/bottlenecks.html
Introgressionhttps://tskit.dev/tutorials/introgression.html
Recapitating a forward simulationhttps://tskit.dev/tutorials/completing_forward_sims.html
Building a forward simulatorhttps://tskit.dev/tutorials/forward_sims.html
Advanced forward simulationshttps://tskit.dev/tutorials/more_forward_sims.html
Tskit and Rhttps://tskit.dev/tutorials/tskitr.html
Developing new tutorialshttps://tskit.dev/tutorials/tutorial_development.html
Tskit for population geneticshttps://tskit.dev/tutorials/popgen.html
Tskit for phylogeneticshttps://tskit.dev/tutorials/phylogen.html
.md https://tskit.dev/tutorials/_sources/args.md
Full ARGshttps://tskit.dev/tutorials/args.html#full-args
Visualizationhttps://tskit.dev/tutorials/args.html#visualization
Local trees and arityhttps://tskit.dev/tutorials/args.html#local-trees-and-arity
SPRs and recombinationhttps://tskit.dev/tutorials/args.html#sprs-and-recombination
Calculating likelihoodshttps://tskit.dev/tutorials/args.html#calculating-likelihoods
Simplificationhttps://tskit.dev/tutorials/args.html#simplification
Disadvantages of Full ARGshttps://tskit.dev/tutorials/args.html#disadvantages-of-full-args
ARG formats and tskithttps://tskit.dev/tutorials/args.html#arg-formats-and-tskit
Working with ARGs in tskithttps://tskit.dev/tutorials/args.html#working-with-args-in-tskit
Graph traversalhttps://tskit.dev/tutorials/args.html#graph-traversal
Traversing parent nodeshttps://tskit.dev/tutorials/args.html#traversing-parent-nodes
Traversing child nodeshttps://tskit.dev/tutorials/args.html#traversing-child-nodes
Counting unique childrenhttps://tskit.dev/tutorials/args.html#counting-unique-children
Other graph analysishttps://tskit.dev/tutorials/args.html#other-graph-analysis
Other softwarehttps://tskit.dev/tutorials/args.html#other-software
#https://tskit.dev/tutorials/args.html#args-as-tree-sequences
tree sequencehttps://tskit.dev/tutorials/what_is.html#sec-what-is
Nodeshttps://tskit.dev/tutorials/terminology_and_concepts.html#sec-terminology-nodes
Edgeshttps://tskit.dev/tutorials/terminology_and_concepts.html#sec-terminology-edges
directed graphhttps://en.wikipedia.org/wiki/Directed_graph
this paperhttp://dx.doi.org/10.1093/genetics/iyae100
#https://tskit.dev/tutorials/args.html#full-args
Griffiths & Marjoram (1997)https://research.monash.edu/en/publications/an-ancestral-recombination-graph
often usedhttps://doi.org/10.1086%2F508901
tskithttps://tskit.dev
msprime.sim_ancestry()https://tskit.dev/msprime/docs/stable/api.html#msprime.sim_ancestry
in the msprime docshttps://tskit.dev/msprime/docs/stable/ancestry.html#sec-ancestry-full-arg
#https://tskit.dev/tutorials/args.html#visualization
NODE_IS_RE_EVENThttps://tskit.dev/msprime/docs/stable/api.html#msprime.msprime.NODE_IS_RE_EVENT
Visualizationhttps://tskit.dev/tutorials/viz.html#sec-tskit-viz
plotted as graphshttps://tskit.dev/tutorials/viz.html#sec-tskit-viz-other-graph
tskit_arg_visualiserhttps://github.com/kitchensjn/tskit_arg_visualizer
#https://tskit.dev/tutorials/args.html#local-trees-and-arity
simplifyhttps://tskit.dev/tutorials/args.html#sec-args-simplification
more compacthttps://tskit.dev/tutorials/args.html#sec-args-disadvantages
subtree-prune-and-regraft (SPR)https://tskit.dev/tutorials/terminology_and_concepts.html#sec-concepts-sprs
Hudson (1983)https://doi.org/10.1016/0040-5809(83)90013-8
#https://tskit.dev/tutorials/args.html#sprs-and-recombination
#https://tskit.dev/tutorials/args.html#calculating-likelihoods
msprime.log_arg_likelihood()https://tskit.dev/msprime/docs/stable/api.html#msprime.log_arg_likelihood
#https://tskit.dev/tutorials/args.html#simplification
simplifyhttps://tskit.dev/tutorials/simplification.html#sec-simplification
#https://tskit.dev/tutorials/args.html#disadvantages-of-full-args
msprimehttps://tskit.dev/software/msprime.html
SLiMhttps://tskit.dev/software/SLiM.html
Griffiths (1991)https://www.jstor.org/stable/4355649
#https://tskit.dev/tutorials/args.html#arg-formats-and-tskit
nodeshttps://tskit.dev/tskit/docs/stable/glossary.html#sec-data-model-definitions-node
lefthttps://tskit.dev/tskit/docs/stable/python-api.html#tskit.Edge.left
righthttps://tskit.dev/tskit/docs/stable/python-api.html#tskit.Edge.right
gARGshttps://www.biorxiv.org/content/10.1101/2023.11.03.565466v1
Gene conversionhttps://tskit.dev/msprime/docs/stable/ancestry.html#sec-ancestry-gene-conversion
inferrred recombining viral genealogieshttps://www.biorxiv.org/content/10.1101/2023.06.08.544212v1
#https://tskit.dev/tutorials/args.html#working-with-args-in-tskit
#https://tskit.dev/tutorials/args.html#graph-traversal
TreeSequence.edge_diffs()https://tskit.dev/tskit/docs/stable/python-api.html#tskit.TreeSequence.edge_diffs
TreeSequence.trees()https://tskit.dev/tskit/docs/stable/python-api.html#tskit.TreeSequence.trees
TreeSequence.nodes()https://tskit.dev/tskit/docs/stable/python-api.html#tskit.TreeSequence.nodes
TreeSequence.nodes()https://tskit.dev/tskit/docs/stable/python-api.html#tskit.TreeSequence.nodes
#https://tskit.dev/tutorials/args.html#traversing-parent-nodes
orderedhttps://tskit.dev/tskit/docs/stable/data-model.html#sec-edge-requirements
#https://tskit.dev/tutorials/args.html#traversing-child-nodes
isolatedhttps://tskit.dev/tskit/docs/stable/data-model.html#sec-data-model-tree-isolated-nodes
roothttps://tskit.dev/tskit/docs/stable/data-model.html#sec-data-model-tree-roots
#https://tskit.dev/tutorials/args.html#counting-unique-children
#https://tskit.dev/tutorials/args.html#other-graph-analysis
networkxhttps://networkx.org/
Visualizationhttps://tskit.dev/tutorials/viz.html#sec-tskit-viz
#https://tskit.dev/tutorials/args.html#other-software
previous Working with Metadata https://tskit.dev/tutorials/metadata.html
next Tree sequences and simulation https://tskit.dev/tutorials/simulation_overview.html
Full ARGshttps://tskit.dev/tutorials/args.html#full-args
Visualizationhttps://tskit.dev/tutorials/args.html#visualization
Local trees and arityhttps://tskit.dev/tutorials/args.html#local-trees-and-arity
SPRs and recombinationhttps://tskit.dev/tutorials/args.html#sprs-and-recombination
Calculating likelihoodshttps://tskit.dev/tutorials/args.html#calculating-likelihoods
Simplificationhttps://tskit.dev/tutorials/args.html#simplification
Disadvantages of Full ARGshttps://tskit.dev/tutorials/args.html#disadvantages-of-full-args
ARG formats and tskithttps://tskit.dev/tutorials/args.html#arg-formats-and-tskit
Working with ARGs in tskithttps://tskit.dev/tutorials/args.html#working-with-args-in-tskit
Graph traversalhttps://tskit.dev/tutorials/args.html#graph-traversal
Traversing parent nodeshttps://tskit.dev/tutorials/args.html#traversing-parent-nodes
Traversing child nodeshttps://tskit.dev/tutorials/args.html#traversing-child-nodes
Counting unique childrenhttps://tskit.dev/tutorials/args.html#counting-unique-children
Other graph analysishttps://tskit.dev/tutorials/args.html#other-graph-analysis
Other softwarehttps://tskit.dev/tutorials/args.html#other-software

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