BQinference

This is a C++ function, used in <code>TINNIKdist</code>, to
infer B and T quartets. Doucumentation if for internal use only.

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>,
and 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>. 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

BQinference function

<dl><dt>pTable</dt>
<dd>a quartet table with p-values</dd>
<dt>C</dt>
<dd>precomputed binomial coefficients</dd>
<dt>Cn4</dt>
<dd>precomputed binomial coefficient</dd>
<dt>n</dt>
<dd>number of taxa</dd>
<dt>Bquartets</dt>
<dd>0/1 vector of initial Bquartets</dd>
<dt>L1</dt>
<dd>vector of recently inferred B quartets</dd>
<dt>lenL1</dt>
<dd>lnegth of L1</dd>
<dt>Nrule1</dt>
<dd>count of inference from rule 1</dd>
<dt>Nrule2</dt>
<dd>count of inference from rule 2</dd>
<dt>cuttops</dt>
<dd>inferred cut topologies</dd></dl>

Arguments

Main loop of B-quartet inference — BQinference

<dl>

<dt>pTable</dt>
<dd>a quartet table with p-values</dd>


<dt>C</dt>
<dd>precomputed binomial coefficients</dd>


<dt>Cn4</dt>
<dd>precomputed binomial coefficient</dd>


<dt>n</dt>
<dd>number of taxa</dd>


<dt>Bquartets</dt>
<dd>0/1 vector of initial Bquartets</dd>


<dt>L1</dt>
<dd>vector of recently inferred B quartets</dd>


<dt>lenL1</dt>
<dd>lnegth of L1</dd>


<dt>Nrule1</dt>
<dd>count of inference from rule 1</dd>


<dt>Nrule2</dt>
<dd>count of inference from rule 2</dd>


<dt>cuttops</dt>
<dd>inferred cut topologies</dd>

</dl>

BQinference: Main loop of B-quartet inference

Description

Usage

Value

Arguments

See Also