Species Tree Inference from Genomic Sequences Using the Log-Det Distance

DOI10.1137/18M1194134zbMath1415.92127arXiv1806.04974WikidataQ101461092 ScholiaQ101461092MaRDI QIDQ5742691

Colby Long, Elizabeth S. Allman, John A. Rhodes

Publication date: 8 May 2019

Published in: SIAM Journal on Applied Algebra and Geometry (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1806.04974

zbMATH Keywords

quadratic formsmixture modelsmultispecies coalescentdistance-based methodsgeneral time-reversible model

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Problems related to evolution (92D15) Protein sequences, DNA sequences (92D20)

Related Items (5)

Identifiability of species network topologies from genomic sequences using the logDet distance ⋮ A stochastic Farris transform for genetic data under the multispecies coalescent with applications to data requirements ⋮ Phylogenomic Models from Tree Symmetries ⋮ Designing weights for quartet-based methods when data are heterogeneous across lineages ⋮ Species tree estimation under joint modeling of coalescence and duplication: sample complexity of quartet methods

Uses Software

• MrBayes
• ASTRAL-II
• STEM-hy
• ASTRID

Cites Work

• Unnamed Item
• MrBayes
• Recovering a tree from the leaf colourations it generates under a Markov model
• Identifiability and reconstructibility of species phylogenies under a modified coalescent
• Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent

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