(Q26777689)

Brant C Faircloth

4

0 references

Scott V. Edwards

Scott V Edwards

1

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Emily Moriarty Lemmon

9

Emily Moriarty Lemmon

0 references

Alan R. Lemmon

10

Alan R Lemmon

0 references

Travis Glenn

6

Travis C Glenn

0 references

Axel Janke

3

Axel Janke

0 references

Charles Cavender Davis

13

Charles C Davis

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author name string

Zhenxiang Xi

2

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John E McCormack

5

0 references

Shaoyuan Wu

8

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Adam D Leaché

11

0 references

Liang Liu

Molecular Phylogenetics and Evolution

12

0 references

language of work or name

English

0 references

publication date

January 2016

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published in

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volume

94

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issue

Pt A

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page(s)

447-62

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cites work

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Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses

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Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses

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A comparative study of SVDquartets and other coalescent-based species tree estimation methods

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Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer

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Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

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Agalma: an automated phylogenomics workflow

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Testing for ancient admixture between closely related populations

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Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow

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Is a new and general theory of molecular systematics emerging?

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Natural selection and phylogenetic analysis

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Hidden likelihood support in genomic data: can forty-five wrongs make a right?

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Automated removal of noisy data in phylogenomic analyses.

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New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

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Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations

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Mammalian evolution may not be strictly bifurcating

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Bayesian inference of species trees from multilocus data

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Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model

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Whole-genome analyses resolve early branches in the tree of life of modern birds

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Speciation with gene flow in equids despite extensive chromosomal plasticity

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Full modeling versus summarizing gene-tree uncertainty: method choice and species-tree accuracy

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Inconsistency of phylogenetic estimates from concatenated data under coalescence

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Coalescent-based genome analyses resolve the early branches of the euarchontoglires.

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Bears in a forest of gene trees: phylogenetic inference is complicated by incomplete lineage sorting and gene flow

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Is recombination a problem for species-tree analyses?

7 January 2021

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How low can you go? The effects of mutation rate on the accuracy of species-tree estimation

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The accuracy of species tree estimation under simulation: a comparison of methods

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The influence of gene flow on species tree estimation: a simulation study

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One thousand two hundred ninety nuclear genes from a genome-wide survey support lungfishes as the sister group of tetrapods

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Phylogenetic analysis in the anomaly zone

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Estimating species phylogenies using coalescence times among sequences.

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

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Coalescent methods are robust to the simultaneous effects of long branches and incomplete lineage sorting

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The frailty of adaptive hypotheses for the origins of organismal complexity

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A Modified Bootscan Algorithm for Automated Identification of Recombinant Sequences and Recombination Breakpoints

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Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design

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Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

7 January 2021

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A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species

7 January 2021

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

7 January 2021

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ASTRAL: genome-scale coalescent-based species tree estimation

7 January 2021

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

7 January 2021

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Phylogenomics resolves the timing and pattern of insect evolution

7 January 2021

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Resolution of the early placental mammal radiation using Bayesian phylogenetics

7 January 2021

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Jaatha: a fast composite-likelihood approach to estimate demographic parameters

7 January 2021

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Computational approaches to species phylogeny inference and gene tree reconciliation

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T-Coffee: A novel method for fast and accurate multiple sequence alignment

7 January 2021

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Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria

7 January 2021

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Error in Phylogenetic Estimation for Bushes in the Tree of Life

7 January 2021

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Resolving difficult phylogenetic questions: why more sequences are not enough

7 January 2021

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Evaluation of methods for detecting recombination from DNA sequences: computer simulations

7 January 2021

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The effect of recombination on the accuracy of phylogeny estimation

7 January 2021

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Recombination in evolutionary genomics

7 January 2021

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OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics

7 January 2021

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Discordance of species trees with their most likely gene trees: a unifying principle.

7 January 2021

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Genealogical trees, coalescent theory and the analysis of genetic polymorphisms

7 January 2021

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Discordance of species trees with their most likely gene trees: the case of five taxa.

7 January 2021

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Recombination and phylogeny: effects and detection

7 January 2021

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Insights into hominid evolution from the gorilla genome sequence

7 January 2021

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Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms

7 January 2021

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The concordance of gene trees and species trees at two linked loci

7 January 2021

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Phyutility: a phyloinformatics tool for trees, alignments and molecular data

7 January 2021

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Analyzing and synthesizing phylogenies using tree alignment graphs

7 January 2021

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

7 January 2021

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Land plant origins and coalescence confusion

7 January 2021

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7 January 2021

The gene tree delusion

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

7 January 2021

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Exploring Tree-Like and Non-Tree-Like Patterns Using Genome Sequences: An Example Using the Inbreeding Plant Species Arabidopsis thaliana (L.) Heynh

7 January 2021

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The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds

7 January 2021

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Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods

7 January 2021

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PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

7 January 2021

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Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles

7 January 2021

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Phylogenomic analyses elucidate the evolutionary relationships of bats

7 January 2021

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Testing hypotheses about the sister group of the passeriformes using an independent 30-locus data set.

7 January 2021

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kdetrees: Non-parametric estimation of phylogenetic tree distributions.

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Fine-scale phylogenetic discordance across the house mouse genome

7 January 2021

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Deciphering ancient rapid radiations

7 January 2021

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Phylotranscriptomic analysis of the origin and early diversification of land plants

7 January 2021

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Reply to Gatesy and Springer: the multispecies coalescent model can effectively handle recombination and gene tree heterogeneity

7 January 2021

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Phylogenomics and coalescent analyses resolve extant seed plant relationships

7 January 2021

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Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies

7 January 2021

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

7 January 2021

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A maximum pseudo-likelihood approach for phylogenetic networks

7 January 2021

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Origin of land plants using the multispecies coalescent model

7 January 2021

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The multispecies coalescent model and land plant origins: a reply to Springer and Gatesy

7 January 2021

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Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3.

7 January 2021

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