dataYeastRokas

<p>A text file dataset for Yeast containing 106 gene trees on 8 taxa  (7 Saccharomyces and 1 Candida outgroup). This is a subset of the data
of Rokas03;textualMSCquartets.</p>

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

dataYeastRokas function

<p>A text file with 106 topological Newick gene trees on the taxa:
 Sbay, Scas, Scer, Sklu, Skud, Smik, Spar, and Calb (outgroup).</p>

Format

Yeast gene tree dataset — dataYeastRokas

Yeast gene tree dataset

dataYeastRokas: Yeast gene tree dataset

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References