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On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods

Systematic biology, 2015-07, Vol.64 (4), p.663-676

2015

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FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization

Bioinformatics (Oxford, England), 2017-03, Vol.33 (5), p.631-639

2017

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

Science (American Association for the Advancement of Science), 2014-12, Vol.346 (6215), p.1337-1337

2014

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Ultra-large alignments using phylogeny-aware profiles

Genome Biology, 2015-06, Vol.16 (1), p.124-124, Article 124

2015

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Unblended disjoint tree merging using GTM improves species tree estimation

BMC genomics, 2020-04, Vol.21 (Suppl 2), p.235-235, Article 235

2020

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PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences

Journal of computational biology, 2015-05, Vol.22 (5), p.377-386

2015

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

PloS one, 2015-06, Vol.10 (6), p.e0129183-e0129183

2015

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

BMC genomics, 2015-10, Vol.16 Suppl 10 (S10), p.S2-S2, Article S2

2015

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

BMC genomics, 2015-10, Vol.16 Suppl 10 (S10), p.S1-S1, Article S1

2015

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Weighted ASTRID: fast and accurate species trees from weighted internode distances

Algorithms for molecular biology, 2023-07, Vol.18 (1), p.6-6, Article 6

2023

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The performance of coalescent-based species tree estimation methods under models of missing data

BMC genomics, 2018-05, Vol.19 (Suppl 5), p.286-286, Article 286

2018

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SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees

Systematic biology, 2012, Vol.61 (1), p.90-106

2012

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

Bioinformatics (Oxford, England), 2015-06, Vol.31 (12), p.i44-i52

2015

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RAxML and FastTree: comparing two methods for large-scale maximum likelihood phylogeny estimation

PloS one, 2011-11, Vol.6 (11), p.e27731-e27731

2011

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SIESTA: enhancing searches for optimal supertrees and species trees

BMC genomics, 2018-05, Vol.19 (Suppl 5), p.252-252, Article 252

2018

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Viewing computer science through citation analysis: Salton and Bergmark Redux

Scientometrics, 2020-10, Vol.125 (1), p.271-287

2020

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A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity

NPJ biofilms and microbiomes, 2016-04, Vol.2 (1), p.16004-16004, Article 16004

2016

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FASTSP: linear time calculation of alignment accuracy

Bioinformatics, 2011-12, Vol.27 (23), p.3250-3258

2011

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Scaling statistical multiple sequence alignment to large datasets

BMC genomics, 2016-11, Vol.17 (Suppl 10), p.764-764, Article 764

2016

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Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees

Science (American Association for the Advancement of Science), 2009-06, Vol.324 (5934), p.1561-1564

2009

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Bioinformatics and Phylogenetics: Seminal Contributions of Bernard Moret

Warnow, Tandy

1st ed. 2019., 2019

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Computing and Combinatorics: 9th Annual International Conference, COCOON 2003, Big Sky, MT, USA, July 25-28, 2003, Proceedings

2003, 2003

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Gene tree parsimony for incomplete gene trees: addressing true biological loss

Algorithms for molecular biology, 2018-01, Vol.13 (1), p.1-1, Article 1

2018

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AOC: Assembling overlapping communities

Quantitative science studies, 2022-12, Vol.3 (4), p.1079-1096

2022

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Simultaneous radiation of bird and mammal lice following the K-Pg boundary

Biology letters (2005), 2018-05, Vol.14 (5), p.20180141-20180141

2018

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On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods

FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization

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

Ultra-large alignments using phylogeny-aware profiles

Unblended disjoint tree merging using GTM improves species tree estimation

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences

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

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

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

Weighted ASTRID: fast and accurate species trees from weighted internode distances

The performance of coalescent-based species tree estimation methods under models of missing data

SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees

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

RAxML and FastTree: comparing two methods for large-scale maximum likelihood phylogeny estimation

SIESTA: enhancing searches for optimal supertrees and species trees

Viewing computer science through citation analysis: Salton and Bergmark Redux

A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity

FASTSP: linear time calculation of alignment accuracy

Scaling statistical multiple sequence alignment to large datasets

Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees

Bioinformatics and Phylogenetics: Seminal Contributions of Bernard Moret

Computing and Combinatorics: 9th Annual International Conference, COCOON 2003, Big Sky, MT, USA, July 25-28, 2003, Proceedings

Gene tree parsimony for incomplete gene trees: addressing true biological loss

AOC: Assembling overlapping communities

Simultaneous radiation of bird and mammal lice following the K-Pg boundary

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