quartetTreeErrorProb

From a gene quartet count concordance factor (qcCF), computes Bayesian posterior probabilities
of the three 4-taxon species tree topologies and the Bayesian posterior probability that the
assumed topology is incorrect, under the assumption that the counts arise from the MSC on some species tree.

Methods for analyzing and using quartets displayed on a collection
of gene trees, primarily to make inferences about the species tree or network
under the multi-species coalescent model. These include quartet hypothesis tests
for the model, as developed by Mitchell et al. (2019) <doi:10.1214/19-EJS1576>,
simplex plots of quartet concordance factors as presented by Allman et al. (2020)
<doi:10.1101/2020.02.13.948083>, species tree inference methods based on quartet
distances of Rhodes (2019) <doi:10.1109/TCBB.2019.2917204> and Yourdkhani and
Rhodes (2019) <doi:10.1007/s11538-020-00773-4>, the NANUQ algorithm for inference
of level-1 species networks of Allman et al. (2019) <doi:10.1186/s13015-019-0159-2>,
the TINNIK algorithm for inference of the tree of blobs of an arbitrary
network of Allman et al.(2022) <doi:10.1007/s00285-022-01838-9>, and
NANUQ+ routines for resolving multifurcations in the tree of blobs to cycles as in
Allman et al.(2024) (forthcoming).
Software announcement by Rhodes et al. (2020) <doi:10.1093/bioinformatics/btaa868>.

John Rhodes

MSCquartets

Analyzing Gene Tree Quartets under the Multi-Species Coalescent

Elizabeth Allman

Hector Banos

Jonathan Mitchell

Kristina Wicke

quartetTreeErrorProb function

<dl><dt>obs</dt>
<dd>vector of counts for 3 topologies</dd>
<dt>model</dt>
<dd><code>"T3"</code> or <code>"T1"</code>, for the models of MAR19;textualMSCquartets describing an unspecified species
tree topology (<code>"T3"</code>), or the topology whose count is the first entry of <code>obs</code> (<code>"T1"</code>)</dd></dl>

Arguments

Bayesian posterior probability of error in 4-taxon unrooted species tree topology estimate — quartetTreeErrorProb

<dl>

<dt>obs</dt>
<dd>vector of counts for 3 topologies</dd>


<dt>model</dt>
<dd><code>"T3"</code> or <code>"T1"</code>, for the models of MAR19;textualMSCquartets describing an unspecified species
tree topology (<code>"T3"</code>), or the topology whose count is the first entry of <code>obs</code> (<code>"T1"</code>)</dd>

</dl>

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quartetTreeErrorProb: Bayesian posterior probability of error in 4-taxon unrooted species tree topology estimate

Description

Usage

Value

Arguments

Details

References

Examples