Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss

DOI10.1007/978-3-030-45257-5_8MaRDI QIDQ5041802zbMATHOpenAlexFDO

Authors Brandon Legried, Erin K. Molloy, Sebastien Roch, Tandy J. Warnow

Publication date 14 October 2022

Published in Lecture Notes in Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/978-3-030-45257-5_8

zbMATH Keywords

estimationidentifiabilitystatistical consistencyASTRALgene duplication and lossspecies trees

Mathematics Subject Classification ID

Genetics and epigenetics (92D10) Problems related to evolution (92D15)

Recommendations

• Comparing methods for species tree estimation with gene duplication and loss
• Species tree estimation under joint modeling of coalescence and duplication: sample complexity of quartet methods
• Reconciling a gene tree to a species tree under the duplication cost model
• Gene tree correction for reconciliation and species tree inference: complexity and algorithms
• Computing the probability of gene trees concordant with the species tree in the multispecies coalescent
• Statistically consistent rooting of species trees under the multispecies coalescent model
• Probabilistic reconstruction of genealogies for polyploid plant species

Cites work

• scientific article; zbMATH DE number 7205091 (Why is no real title available?)
• Comparison of phylogenetic trees
• Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent
• Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent
• Reconstructing the shape of a tree from observed dissimilarity data
• Species trees from gene trees despite a high rate of lateral genetic transfer: a tight bound (extended abstract)
• The coalescent
• The gene evolution model and computing its associated probabilities

Cited in

(7)

• Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models
• Comparing methods for species tree estimation with gene duplication and loss
• QT-GILD: Quartet based gene tree imputation using deep learning improves phylogenomic analyses despite missing data
• Statistically consistent rooting of species trees under the multispecies coalescent model
• Reversible polymorphism-aware phylogenetic models and their application to tree inference
• Species tree estimation under joint modeling of coalescence and duplication: sample complexity of quartet methods
• Fast and accurate species trees from weighted internode distances

Describes a project that uses

Uses Software

• RAxML
• DupTree
• SimPhy
• ASTRAL-II
• PhyloNet
• INDELible
• MulRF
• BUCKy
• ASTRID
• DynaDup
• GitHub

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