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Quartet inference from SNP data under the coalescent model

Bioinformatics, 2014-12, Vol.30 (23), p.3317-3324

2014

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Comparative Performance of Popular Methods for Hybrid Detection using Genomic Data

Systematic biology, 2021-08, Vol.70 (5), p.891-907

2021

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An invariants-based method for efficient identification of hybrid species from large-scale genomic data

BMC ecology and evolution, 2019-05, Vol.19 (1), p.112, Article 112

2019

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HyDe: A Python Package for Genome-Scale Hybridization Detection

Systematic biology, 2018-09, Vol.67 (5), p.821-829

2018

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HyDe: A Python Package for Genome-Scale Hybridization Detection

Systematic biology, 2018-09, Vol.67 (5), p.821

2018

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Assessment of positive selection across SARS-CoV-2 variants via maximum likelihood

PloS one, 2023-09, Vol.18 (9), p.e0291271

2023

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On the effects of selection and mutation on species tree inference

Molecular phylogenetics and evolution, 2023-02, Vol.179, p.107650-107650, Article 107650

2023

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SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data

Bioinformatics, 2018-02, Vol.34 (3), p.407-415

2018

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Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data

Systematic biology, 2018-05, Vol.67 (3), p.439-457

2018

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A phylogenetic approach to inferring the order in which mutations arise during cancer progression

PLoS computational biology, 2022-12, Vol.18 (12), p.e1010560-e1010560

2022

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Implications of gene tree heterogeneity on downstream phylogenetic analyses: A case study employing the Fair Proportion index

PloS one, 2024-04, Vol.19 (4), p.e0300900-e0300900

2024

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Long-Branch Attraction in Species Tree Estimation: Inconsistency of Partitioned Likelihood and Topology-Based Summary Methods

Systematic biology, 2019-03, Vol.68 (2), p.281-297

2019

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Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs

Systematic biology, 2022-02, Vol.71 (2), p.367-381

2022

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Accurate Inference of Tree Topologies from Multiple Sequence Alignments Using Deep Learning

Systematic biology, 2020-03, Vol.69 (2), p.221-233

2020

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STEM: species tree estimation using maximum likelihood for gene trees under coalescence

Bioinformatics, 2009-04, Vol.25 (7), p.971-973

2009

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Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome

Science (American Association for the Advancement of Science), 2022-04, Vol.376 (6589), p.156-162

2022

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Effects of missing data on species tree estimation under the coalescent

Molecular phylogenetics and evolution, 2013-12, Vol.69 (3), p.1057-1062

2013

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Reduced susceptibility to praziquantel among naturally occurring Kenyan isolates of Schistosoma mansoni

PLoS neglected tropical diseases, 2009-08, Vol.3 (8), p.e504-e504

2009

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Rooting phylogenetic trees under the coalescent model using site pattern probabilities

BMC evolutionary biology, 2017-12, Vol.17 (1), p.263, Article 263

2017

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Identification of Hidden Population Structure in Time-Scaled Phylogenies

Systematic biology, 2020-09, Vol.69 (5), p.884-896

2020

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Hypothesis Testing With Rank Conditions in Phylogenetics

Frontiers in genetics, 2021-07, Vol.12, p.664357-664357

2021

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Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias)

Systematic biology, 2021-08, Vol.70 (5), p.908-921

2021

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Nuclear versus mitochondrial DNA: evidence for hybridization in colobine monkeys

BMC evolutionary biology, 2011-03, Vol.11 (1), p.77, Article 77

2011

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Gene tree rooting methods give distributions that mimic the coalescent process

Molecular phylogenetics and evolution, 2014-01, Vol.70, p.63-69

2014

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Distribution of coalescent histories under the coalescent model with gene flow

Molecular phylogenetics and evolution, 2016-12, Vol.105, p.177-192

2016

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Quartet inference from SNP data under the coalescent model

Comparative Performance of Popular Methods for Hybrid Detection using Genomic Data

An invariants-based method for efficient identification of hybrid species from large-scale genomic data

HyDe: A Python Package for Genome-Scale Hybridization Detection

HyDe: A Python Package for Genome-Scale Hybridization Detection

Assessment of positive selection across SARS-CoV-2 variants via maximum likelihood

On the effects of selection and mutation on species tree inference

SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data

Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data

A phylogenetic approach to inferring the order in which mutations arise during cancer progression

Implications of gene tree heterogeneity on downstream phylogenetic analyses: A case study employing the Fair Proportion index

Long-Branch Attraction in Species Tree Estimation: Inconsistency of Partitioned Likelihood and Topology-Based Summary Methods

Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs

Accurate Inference of Tree Topologies from Multiple Sequence Alignments Using Deep Learning

STEM: species tree estimation using maximum likelihood for gene trees under coalescence

Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome

Effects of missing data on species tree estimation under the coalescent

Reduced susceptibility to praziquantel among naturally occurring Kenyan isolates of Schistosoma mansoni

Rooting phylogenetic trees under the coalescent model using site pattern probabilities

Identification of Hidden Population Structure in Time-Scaled Phylogenies

Hypothesis Testing With Rank Conditions in Phylogenetics

Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias)

Nuclear versus mitochondrial DNA: evidence for hybridization in colobine monkeys

Gene tree rooting methods give distributions that mimic the coalescent process

Distribution of coalescent histories under the coalescent model with gene flow

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