blobDistance

From gene quartet counts, computes NANUQ or modNANUQ distances between groups
of taxa (which should be those around a multifurcation in a tree of blobs.
If these groups are not singletons, averaging is done over group elements.

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

blobDistance function

<dl><dt>pTable</dt>
<dd>table of giving empirical gene quartet counts for the taxa on tree, with columns p_star and p_test</dd>
<dt>taxa</dt>
<dd>a list of taxon names, who positions are used in 'groups'</dd>
<dt>groupvec</dt>
<dd>taxon groups encoded in vector</dd>
<dt>test</dt>
<dd>to be used for detecting hybridizations in quartete ("T3" or "cut")</dd>
<dt>alpha</dt>
<dd>test level for p_test</dd>
<dt>beta</dt>
<dd>test level for p_star</dd>
<dt>dist</dt>
<dd>the distance to compute, either "NANUQ" or "modNANUQ"</dd></dl>

Arguments

Compute empirical distance between taxon groups. — blobDistance

<dl>

<dt>pTable</dt>
<dd>table of giving empirical gene quartet counts for the taxa on tree, with columns p_star and p_test</dd>


<dt>taxa</dt>
<dd>a list of taxon names, who positions are used in 'groups'</dd>


<dt>groupvec</dt>
<dd>taxon groups encoded in vector</dd>


<dt>test</dt>
<dd>to be used for detecting hybridizations in quartete ("T3" or "cut")</dd>


<dt>alpha</dt>
<dd>test level for p_test</dd>


<dt>beta</dt>
<dd>test level for p_star</dd>


<dt>dist</dt>
<dd>the distance to compute, either "NANUQ" or "modNANUQ"</dd>

</dl>

blobDistance: Compute empirical distance between taxon groups.

Description

Usage

Value

Arguments