4.5 Article

Gene tree quality affects empirical coalescent branch length estimation

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

Collapsing dubiously resolved gene-tree branches in phylogenomic coalescent analyses

Mark P. Simmons et al.

Summary: In this study, the impact of alternative methods for collapsing gene-tree branches on species-tree inference was quantified for seven empirical datasets. It was found that the choice of branch-collapsing methods significantly influences species-tree inference, with certain methods enhancing branch support.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2021)

Article Evolutionary Biology

Divergence and support among slightly suboptimal likelihood gene trees

Mark P. Simmons et al.

CLADISTICS (2020)

Article Biochemistry & Molecular Biology

A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis

Tomas Flouri et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Ornithology

Whole genome phylogeny of Gallus: introgression and data-type effects

George P. Tiley et al.

AVIAN RESEARCH (2020)

Article Biochemistry & Molecular Biology

RAD sequencing resolves the phylogeny, taxonomy and biogeography of Trichophoreae despite a recent rapid radiation (Cyperaceae)

Etienne Leveille-Bourret et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2020)

Article Biodiversity Conservation

Phylogenetic Signal of Indels and the Neoavian Radiation

Peter Houde et al.

DIVERSITY-BASEL (2019)

Article Evolutionary Biology

To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods

Erin K. Molloy et al.

SYSTEMATIC BIOLOGY (2018)

Article Biochemistry & Molecular Biology

Coalescent Analysis of Phylogenomic Data Confidently Resolves the Species Relationships in the Anopheles gambiae Species Complex

Yuttapong Thawornwattana et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Biochemistry & Molecular Biology

Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction

Erfan Sayyari et al.

MOLECULAR BIOLOGY AND EVOLUTION (2017)

Article Biochemistry & Molecular Biology

In silico phylogenomics using complete genomes: a case study on the evolution of hominoids

Igor Rodrigues Costa et al.

GENOME RESEARCH (2016)

Article Biochemistry & Molecular Biology

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

Erfan Sayyari et al.

MOLECULAR BIOLOGY AND EVOLUTION (2016)

Article Biochemistry & Molecular Biology

The gene tree delusion

Mark S. Springer et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2016)

Article Biochemical Research Methods

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

Siavash Mirarab et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased

Zhenxiang Xi et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2015)

Article Multidisciplinary Sciences

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

Richard O. Prum et al.

NATURE (2015)

Article Biochemical Research Methods

ASTRAL: genome-scale coalescent-based species tree estimation

S. Mirarab et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis

BIOINFORMATICS (2014)

Article Biochemistry & Molecular Biology

Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

John Gatesy et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2014)

Article Multidisciplinary Sciences

Statistical binning enables an accurate coalescent-based estimation of the avian tree

Siavash Mirarab et al.

SCIENCE (2014)

Article Evolutionary Biology

Conserved Genes, Sampling Error, and Phylogenomic Inference

Ricardo Betancur-R et al.

SYSTEMATIC BIOLOGY (2014)

Article Evolutionary Biology

Bias in Tree Searches and its Consequences for Measuring Group Supports

Pablo A. Goloboff et al.

SYSTEMATIC BIOLOGY (2014)

Letter Plant Sciences

Land plant origins and coalescence confusion

Mark S. Springer et al.

TRENDS IN PLANT SCIENCE (2014)

Article Biotechnology & Applied Microbiology

Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition

Claudia C. Weber et al.

GENOME BIOLOGY (2014)

Article Biochemical Research Methods

Naive binning improves phylogenomic analyses

Md Shamsuzzoha Bayzid et al.

BIOINFORMATICS (2013)

Article Multidisciplinary Sciences

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

Sen Song et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Evolutionary Biology

Homoplastic microinversions and the avian tree of life

Edward L. Braun et al.

BMC EVOLUTIONARY BIOLOGY (2011)

Article Evolutionary Biology

The Accuracy of Species Tree Estimation under Simulation: A Comparison of Methods

Adam D. Leache et al.

SYSTEMATIC BIOLOGY (2011)

Article Evolutionary Biology

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

Liang Liu et al.

BMC EVOLUTIONARY BIOLOGY (2010)

Editorial Material Ecology

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

Scott V. Edwards

EVOLUTION (2009)

Review Biochemistry & Molecular Biology

Coalescent methods for estimating phylogenetic trees

Liang Liu et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2009)

Article Evolutionary Biology

What Is the Danger of the Anomaly Zone for Empirical Phylogenetics?

Huateng Huang et al.

SYSTEMATIC BIOLOGY (2009)

Review Ecology

Gene tree discordance, phylogenetic inference and the multispecies coalescent

James H. Degnan et al.

TRENDS IN ECOLOGY & EVOLUTION (2009)

Article Evolutionary Biology

Inconsistency of phylogenetic estimates from concatenated data under coalescence

Laura Salter Kubatko et al.

SYSTEMATIC BIOLOGY (2007)

Article Genetics & Heredity

Discordance of species trees with their most likely gene trees

James H. Degnan et al.

PLOS GENETICS (2006)

Article Biochemistry & Molecular Biology

Molecular polytomies

JB Slowinski

MOLECULAR PHYLOGENETICS AND EVOLUTION (2001)

Article Biochemistry & Molecular Biology

Ancestral lineages of arbuscular mycorrhizal fungi (Glomales)

D Redecker et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2000)