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List of works by Tandy Warnow

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

scientific article

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

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

scientific article published on 20 April 2016

A roadmap for global synthesis of the plant tree of life

scientific article published on 30 March 2018

A simulation study comparing supertree and combined analysis methods using SMIDGen

scientific article

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

scientific article published on June 2015

ASTRAL: genome-scale coalescent-based species tree estimation

scientific article

ASTRID: Accurate Species TRees from Internode Distances

scientific article

Addressing Polymorphism in Linguistic Phylogenetics

scientific article published on 9 April 2024

Advances in phylogeny reconstruction from gene order and content data

scientific article published in January 2005

Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles ⬇️

scientific article published on October 28, 2011

An analytical upper bound on the number of loci required for all splits of a species tree to appear in a set of gene trees

scientific article

An experimental study of Quartets MaxCut and other supertree methods ⬇️

scientific article

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee).

scientific article

BBCA: Improving the scalability of *BEAST using random binning

scientific article

Barking up the wrong treelength: the impact of gap penalty on alignment and tree accuracy

scientific article published on 01 January 2009

Benchmark datasets and software for developing and testing methods for large-scale multiple sequence alignment and phylogenetic inference ⬇️

scientific article published on November 18, 2010

Better methods for solving parsimony and compatibility.

scientific article published in January 1998

Chemical phylogenetics of histone deacetylases

scientific article

Co-citations in context: Disciplinary heterogeneity is relevant

scientific article published in 2020

Concatenation Analyses in the Presence of Incomplete Lineage Sorting

scientific article published on 22 May 2015

Constrained incremental tree building: new absolute fast converging phylogeny estimation methods with improved scalability and accuracy

scientific article published on 06 February 2019

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

scientific article published on 10 February 2020

DACTAL: divide-and-conquer trees (almost) without alignments ⬇️

scientific article published on June 15, 2012

DISCO+QR: rooting species trees in the presence of GDL and ILS

scientific article published in January 2023

Data access for the 1,000 Plants (1KP) project

scientific article

Disk covering methods improve phylogenomic analyses

scientific article

Distance-based genome rearrangement phylogeny

scientific article published on 4 October 2006

Estimating Optimal Species Trees from Incomplete Gene Trees Under Deep Coalescence ⬇️

scientific article published on June 1, 2012

Evaluating Statistical Multiple Sequence Alignment in Comparison to Other Alignment Methods on Protein Data Sets

scientific article published in May 2019

Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting

scientific article

Fast and accurate methods for phylogenomic analyses ⬇️

scientific article published on October 5, 2011

Fast phylogenetic methods for the analysis of genome rearrangement data: an empirical study

scientific article

FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models

scientific article published on 01 July 2020

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

scientific article published on 23 September 2016

FastSP: linear time calculation of alignment accuracy

scientific article

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

scientific article published on 19 January 2018

HIPPI: highly accurate protein family classification with ensembles of HMMs

scientific article

High diversity of picornaviruses in rats from different continents revealed by deep sequencing

scientific article

In Memoriam Eugene L. Lawler

scholarly article by Dan Gustfield published in January 1994

Indo-European and Computational Cladistics

Large-Scale Multiple Sequence Alignment and the Maximum Weight Trace Alignment Merging Problem

scientific article published in May 2023

Large-scale multiple sequence alignment and tree estimation using SATé.

scientific article published on January 2014

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

scientific article published on 01 March 2019

MRL and SuperFine+MRL: new supertree methods

scientific article published on 26 January 2012

Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows

scientific article published on 01 May 2019

Multiple sequence alignment: a major challenge to large-scale phylogenetics

scientific article

NJMerge: A Generic Technique for Scaling Phylogeny Estimation Methods and Its Application to Species Trees

scholarly article by Erin K. Molloy & Tandy Warnow published 2018 in Lecture Notes in Computer Science

Naive binning improves phylogenomic analyses

scientific article published on 09 July 2013

Non-parametric correction of estimated gene trees using TRACTION

scientific article published on 04 January 2020

OCTAL: Optimal Completion of gene trees in polynomial time.

scientific article

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

scientific article

PASTA for proteins

scientific article published on 01 November 2018

PASTA: Ultra-Large Multiple Sequence Alignment

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

scientific article published on 30 December 2014

Pattern identification in biogeography

scientific article published in October 2006

Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages

scholarly article by Luay Nakhleh et al published 2005 in Language

Phylogenetic networks: modeling, reconstructibility, and accuracy

scientific article published in January 2004

Phylogenomic analyses data of the avian phylogenomics project

scientific article

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

scientific article published on 2 October 2015

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

article

Phylogenomics from Whole Genome Sequences Using aTRAM.

scientific article published on 25 January 2017

Phylogeny Estimation Given Sequence Length Heterogeneity

scientific article published on 21 July 2020

Phylotranscriptomic analysis of the origin and early diversification of land plants

scientific article

Primates, Lice and Bacteria: Speciation and Genome Evolution in the Symbionts of Hominid Lice

scientific article published on 14 April 2017

Profile Hidden Markov Models are Not Identifiable

scientific article published on 14 August 2019

QR-STAR: A Polynomial-Time Statistically Consistent Method for Rooting Species Trees Under the Coalescent

scientific article published in November 2023

RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation ⬇️

scientific article published on November 21, 2011

Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees

scientific article published in June 2009

Re-evaluating Deep Neural Networks for Phylogeny Estimation: The Issue of Taxon Sampling

scientific article published in 2022

Rec-I-DCM3: a fast algorithmic technique for reconstructing large phylogenetic trees

scientific article published in January 2004

Reconstructing reticulate evolution in species-theory and practice

scientific article published in July 2005

Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree".

scientific article published on October 2015

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".

scientific article published on September 2015

SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees

scientific article published in December 2011

SCAMPP: Scaling Alignment-Based Phylogenetic Placement to Large Trees

scientific article published in March 2023

SIESTA: enhancing searches for optimal supertrees and species trees.

scientific article published on 8 May 2018

SVDquest: Improving SVDquartets species tree estimation using exact optimization within a constrained search space

scientific article published on 9 March 2018

Scaling statistical multiple sequence alignment to large datasets

scientific article

Short quartet puzzling: a new quartet-based phylogeny reconstruction algorithm.

scientific article published in January 2008

Standard maximum likelihood analyses of alignments with gaps can be statistically inconsistent

scientific article

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

scientific article

Statistically Consistent Estimation of Rooted and Unrooted Level-1 Phylogenetic Networks from SNP Data

Statistically Consistent Rooting of Species Trees Under the Multispecies Coalescent Model

Statistically based postprocessing of phylogenetic analysis by clustering

scientific article published in January 2002

Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge

scientific article published on 19 July 2019

SuperFine: Fast and Accurate Supertree Estimation ⬇️

scientific article published on September 20, 2011

TIPP: taxonomic identification and phylogenetic profiling

scientific article

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)

scientific article

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference ⬇️

scientific article

The accuracy of fast phylogenetic methods for large datasets

scientific article published on 01 January 2002

The development and application of bioinformatics core competencies to improve bioinformatics training and education

scientific article published in February 2018

The impact of multiple protein sequence alignment on phylogenetic estimation

scientific article

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

scientific article

To include or not to include: The Impact of Gene Filtering on Species Tree Estimation Methods

scientific article published on 15 September 2017

Towards the development of computational tools for evaluating phylogenetic network reconstruction methods.

scientific article published in January 2003

TreeMerge: a new method for improving the scalability of species tree estimation methods

scientific article published on 01 July 2019

Treelength Optimization for Phylogeny Estimation ⬇️

scientific article published on March 19, 2012

Two strikes against perfect phylogeny

scholarly article by Hans L. Bodlaender et al published 1992 in Lecture Notes in Computer Science

Ultra-Large Alignments Using Ensembles of Hidden Markov Models

Ultra-large alignments using phylogeny-aware profiles

scientific article published on 16 June 2015

Unblended disjoint tree merging using GTM improves species tree estimation

scientific article published on 16 April 2020

Unidentifiable divergence times in rates-across-sites models

scientific article

Using Constrained-INC for Large-scale Gene Tree and Species Tree Estimation

scientific article published on 14 May 2020

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

scientific article published on 18 June 2015

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

scientific article

Why sequence all eukaryotes?

scientific article published on 01 January 2022

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