A package for analyzing quartets displayed on gene trees, under the multispecies coalescent (MSC) model and network multispecies coalescet model (NMSC).
Maintainer: John Rhodes j.rhodes@alaska.edu (ORCID)
Authors:
Elizabeth Allman esallman@alaska.edu
Hector Banos hbassnos@gmail.com
Jonathan Mitchell jonathanmitchell88@gmail.com
Kristina Wicke kristina.wicke@njit.edu
This package contains routines to analyze a collection of gene trees through the displayed quartets on them.
A quartet count concordance factor (qcCF) for a set of 4 taxa is the triple of counts of the three possible resolved quartet trees on those taxa across some set of gene trees. The major routines in this package can:
Tabulate all qcCFs for a collection of gene trees.
Perform hypothesis tests of whether one or more qcCFs are consistent with the MSC model on a species tree MAR19MSCquartets.
Produce simplex plots showing all estimated CFs as well as results of hypothesis tests AMR2020MSCquartets.
Infer a species tree using the qcCFs via the QDC and WQDC methods Rho19,YR19MSCquartets.
Infer a level-1 species network via the NANUQ method ABR19MSCquartets.
Infer the tree of blobs for a species network via the TINNiK method ABMR22MSCquartets,ABMR24MSCquartets.
Resolove multifurcations in a tree of blobs to cycles via NANUQ+ routines ABRW24MSCquartets.
As discussed in the cited works, the inference methods for species trees and networks are statistically consistent under the MSC and Network MSC respectively.
This package, and the theory on which it is based, allows gene trees to have missing taxa (i.e., not all gene trees display all the taxa). It does require that each subset of 4 taxa is displayed on at least one of the gene trees.
Several gene tree data sets, simulated and empirical, are included.
In publications please cite the software announcement RBMA2020MSCquartets, as well as the appropriate paper(s) above developing the theory behind the routines you used.
RBMA2020MSCquartets
MAR19MSCquartets
AMR2020MSCquartets
Rho19MSCquartets
YR19MSCquartets
ABR19MSCquartets
ABMR22MSCquartets
ABMR24MSCquartets
ABRW24MSCquartets