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1

A comparison of phylogenetic reconstruction methods on an Indo-European dataset

Luay Nakhleh, Tandy Warnow, Don Ringe, Steven N. Evans

Journal:

Transactions of the Philological Society

Year:

2005

Language:

english

File:

PDF, 313 KB

english, 2005

2

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

Luay Nakhleh, Don Ringe and Tandy Warnow

Journal:

Year:

2005

Language:

english

File:

PDF, 4.42 MB

english, 2005

3

Kaikoura tree theorems: Computing the maximum agreement subtree

Mike Steel, Tandy Warnow

Journal:

Information Processing Letters

Year:

1993

Language:

english

File:

PDF, 551 KB

english, 1993

4

Indo-European and Computational Cladistics

Don Ringe, Tandy Warnow, Ann Taylor

Journal:

Transactions of the Philological Society

Year:

2002

Language:

english

File:

PDF, 704 KB

english, 2002

5

High-Performance Algorithm Engineering for Computational Phylogenetics

Bernard M. E. Moret, David A. Bader, Tandy Warnow

Journal:

The Journal of Supercomputing

Year:

2002

Language:

english

File:

PDF, 129 KB

english, 2002

6

Tutorial on Computational Linguistic Phylogeny

Johanna Nichols, Tandy Warnow

Journal:

Language and Linguistics Compass

Year:

2008

Language:

english

File:

PDF, 331 KB

english, 2008

7

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

Nakhleh, Luay, Ringe, Donald A., Warnow, Tandy

Journal:

Year:

2005

Language:

english

File:

PDF, 423 KB

english, 2005

8

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

Nguyen, Nam-Phuong, Warnow, Tandy, Pop, Mihai, White, Bryan

Journal:

npj Biofilms and Microbiomes

Year:

2016

Language:

english

File:

PDF, 1.37 MB

english, 2016

9

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

Lawrence H. Uricchio,Tandy Warnow,Noah A. Rosenberg

Journal:

BMC Bioinformatics

Year:

2016

Language:

english

File:

PDF, 733 KB

english, 2016

10

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

Vachaspati, Pranjal, Warnow, Tandy

Journal:

Molecular Phylogenetics and Evolution

Year:

2018

Language:

english

File:

PDF, 983 KB

english, 2018

11

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

Bayzid, Md Shamsuzzoha, Warnow, Tandy

Journal:

Algorithms for Molecular Biology

Year:

2018

Language:

english

File:

PDF, 1.88 MB

english, 2018

12

A few logs suffice to build (almost) all trees (I)

Péter L. Erdős, Michael A. Steel, László A. Székely, Tandy J. Warnow

Journal:

Random Structures & Algorithms

Year:

1999

Language:

english

File:

PDF, 348 KB

english, 1999

13

Determining the Evolutionary Tree Using Experiments

Sampath K. Kannan, Eugene L. Lawler, Tandy J. Warnow

Journal:

Journal of Algorithms

Year:

1996

Language:

english

File:

PDF, 209 KB

english, 1996

14

Steps toward accurate reconstructions of phylogenies from gene-order data

Bernard M.E. Moret, Jijun Tang, Li-San Wang, Tandy Warnow

Journal:

Journal of Computer and System Sciences

Year:

2002

Language:

english

File:

PDF, 357 KB

english, 2002

15

Minimizing phylogenetic number to find good evolutionary trees

Leslie Ann Goldberg, Paul W. Goldberg, Cynthia A. Phillips, Elizabeth Sweedyk, Tandy Warnow

Journal:

Discrete Applied Mathematics

Year:

1996

Language:

english

File:

PDF, 2.01 MB

english, 1996

16

The asymmetric median tree — A new model for building consensus trees

Cynthia Phillips, Tandy J. Warnow

Journal:

Discrete Applied Mathematics

Year:

1996

Language:

english

File:

PDF, 1.89 MB

english, 1996

17

Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining

Katherine St. John, Tandy Warnow, Bernard M.E Moret, Lisa Vawter

Journal:

Journal of Algorithms

Year:

2003

Language:

english

File:

PDF, 169 KB

english, 2003

18

The hardness of perfect phylogeny, feasible register assignment and other problems on thin colored graphs

Hans L. Bodlaender, Michael R. Fellows, Michael T. Hallett, H.Todd Wareham, Tandy J. Warnow

Journal:

Theoretical Computer Science

Year:

2000

Language:

english

File:

PDF, 271 KB

english, 2000

19

A few logs suffice to build (almost) all trees: Part II

Péter L. Erdo&amp, #x030B, s, Michael A. Steel, LászlóA. Székely, Tandy J. Warnow

Journal:

Theoretical Computer Science

Year:

1999

Language:

english

File:

PDF, 2.36 MB

english, 1999

20

Fast and accurate methods for phylogenomic analyses

Jimmy Yang, Tandy Warnow

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 232 KB

english, 2011

21

A simulation study comparing supertree and combined analysis methods using SMIDGen

M Shel Swenson, François Barbançon, Tandy Warnow, C Randal Linder

Journal:

Algorithms for Molecular Biology

Year:

2010

Language:

english

File:

PDF, 1.49 MB

english, 2010

22

An experimental study of Quartets MaxCut and other supertree methods

M Shel Swenson, Rahul Suri, C Randal Linder, Tandy Warnow

Journal:

Algorithms for Molecular Biology

Year:

2011

Language:

english

File:

PDF, 588 KB

english, 2011

23

Distance-Based Genome Rearrangement Phylogeny

Li-San Wang, Tandy Warnow, Bernard M. E. Moret, Robert K. Jansen, Linda A. Raubeson

Journal:

Journal of Molecular Evolution

Year:

2006

Language:

english

File:

PDF, 251 KB

english, 2006

24

Preface

Tandy Warnow, Binhai Zhu

Journal:

Theoretical Computer Science

Year:

2004

Language:

english

File:

PDF, 115 KB

english, 2004

25

Chemical phylogenetics of histone deacetylases

Bradner, James E, West, Nathan, Grachan, Melissa L, Greenberg, Edward F, Haggarty, Stephen J, Warnow, Tandy, Mazitschek, Ralph

Journal:

Nature Chemical Biology

Year:

2010

Language:

english

File:

PDF, 536 KB

english, 2010

26

Analyzing the Order of Items in Manuscripts ofThe Canterbury Tales

Matthew Spencer, Barbara Bordalejo, Li-San Wang, Adrian C. Barbrook, Linne R. Mooney, Peter Robinson, Tandy Warnow, Christopher J. Howe

Journal:

Language Resources and Evaluation

Year:

2003

Language:

english

File:

PDF, 98 KB

english, 2003

27

MRL and SuperFine+MRL: new supertree methods

Nam Nguyen, Siavash Mirarab, Tandy Warnow

Journal:

Algorithms for Molecular Biology

Year:

2012

Language:

english

File:

PDF, 313 KB

english, 2012

28

[ACM Press the eighth annual international conference - San Diego, California, USA (2004.03.27-2004.03.31)] Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04 - Reconstructing reticulate evolution in species

Nakhleh, Luay, Warnow, Tandy, Linder, C. Randal

Year:

2004

Language:

english

File:

PDF, 234 KB

english, 2004

29

A Fast Algorithm for the Computation and Enumeration of Perfect Phylogenies

Kannan, Sampath, Warnow, Tandy

Journal:

SIAM Journal on Computing

Year:

1997

Language:

english

File:

PDF, 274 KB

english, 1997

30

Tree Reconstruction from Partial Orders

Kannan, Sampath K., Warnow, Tandy J.

Journal:

SIAM Journal on Computing

Year:

1995

Language:

english

File:

PDF, 1.23 MB

english, 1995

31

Computing the Local Consensus of Trees

Kannan, Sampath, Warnow, Tandy, Yooseph, Shibu

Journal:

SIAM Journal on Computing

Year:

1998

Language:

english

File:

PDF, 436 KB

english, 1998

32

Triangulating 3-Colored Graphs

Kannan, Sampath K., Warnow, Tandy J.

Journal:

SIAM Journal on Discrete Mathematics

Year:

1992

Language:

english

File:

PDF, 1.29 MB

english, 1992

33

Triangulating Vertex-Colored Graphs

McMorris, F. R., Warnow, Tandy J., Wimer, Thomas

Journal:

SIAM Journal on Discrete Mathematics

Year:

1994

Language:

english

File:

PDF, 1.55 MB

english, 1994

34

[Lecture Notes in Computer Science] Algorithms in Bioinformatics Volume 5724 || Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes

Salzberg, Steven L., Warnow, Tandy

Year:

2009

Language:

english

File:

PDF, 460 KB

english, 2009

35

[Lecture Notes in Computer Science] Algorithms in Bioinformatics Volume 5724 || A Simple, Practical and Complete $O(\frac{n^3}{ \log n})$ -Time Algorithm for RNA Folding Using the Four-Russians Speedup

Salzberg, Steven L., Warnow, Tandy

Year:

2009

Language:

english

File:

PDF, 245 KB

english, 2009

36

[Lecture Notes in Computer Science] Algorithms in Bioinformatics Volume 5724 ||

Salzberg, Steven L., Warnow, Tandy

Year:

2009

Language:

english

File:

PDF, 9.38 MB

english, 2009

37

Mathematical Approaches to Comparative Linguistics

Journal:

Proceedings of the National Academy of Sciences

Year:

1997

Language:

english

File:

PDF, 1.18 MB

english, 1997

38

[Lecture Notes in Computer Science] Computing and Combinatorics Volume 2697 || Genomic Distances under Deletions and Insertions

Warnow, Tandy, Zhu, Binhai

Year:

2003

Language:

english

File:

PDF, 403 KB

english, 2003

39

Short Quartet Puzzling: A New Quartet-Based Phylogeny Reconstruction Algorithm

Snir, Sagi, Warnow, Tandy, Rao, Satish

Journal:

Journal of Computational Biology

Year:

2008

Language:

english

File:

PDF, 279 KB

english, 2008

40

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

Yu, Yun, Warnow, Tandy, Nakhleh, Luay

Journal:

Journal of Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.03 MB

english, 2011

41

Pattern Identification in Biogeography

Ganapathy, Ganeshkumar, Goodson, Barbara, Jansen, Robert, Le, Hai-son, Ramachandran, Vijaya, Warnow, Tandy

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 865 KB

english, 2006

42

Disk-Covering, a Fast-Converging Method for Phylogenetic Tree Reconstruction

Huson, Daniel H., Nettles, Scott M., Warnow, Tandy J.

Journal:

Journal of Computational Biology

Year:

1999

Language:

english

File:

PDF, 289 KB

english, 1999

43

Constructing phylogenetic trees efficiently using compatibility criteria

Warnow, Tandy J.

Journal:

New Zealand Journal of Botany

Year:

1993

Language:

english

File:

PDF, 793 KB

english, 1993

44

Phylotranscriptomic analysis of the origin and early diversification of land plants

Wickett, Norman J., Mirarab, Siavash, Nguyen, Nam, Warnow, Tandy, Carpenter, Eric, Matasci, Naim, Ayyampalayam, Saravanaraj, Barker, Michael S., Burleigh, J. Gordon, Gitzendanner, Matthew A., Ruhfel,

Journal:

Proceedings of the National Academy of Sciences

Year:

2014

Language:

english

File:

PDF, 954 KB

english, 2014

45

Constructing Evolutionary Trees in the Presence of Polymorphic Characters

Bonet, Maria, Phillips, Cynthia, Warnow, Tandy, Yooseph, Shibu

Journal:

SIAM Journal on Computing

Year:

1999

Language:

english

File:

PDF, 465 KB

english, 1999

46

Reconstructing Reticulate Evolution in Species—Theory and Practice

Nakhleh, Luay, Warnow, Tandy, Linder, C. Randal, John, Katherine St.

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 175 KB

english, 2005

47

Reconstructing Chromosomal Evolution

Wang, Li-San, Warnow, Tandy

Journal:

SIAM Journal on Computing

Year:

2006

Language:

english

File:

PDF, 378 KB

english, 2006

48

Better Methods for Solving Parsimony and Compatibility

BONET, MARIA, STEEL, MIKE, WARNOW, TANDY, YOOSEPH, SHIBU

Journal:

Journal of Computational Biology

Year:

1998

Language:

english

File:

PDF, 2.35 MB

english, 1998

49

[Lecture Notes in Computer Science] Computing and Combinatorics Volume 2697 || The Complexity of Boolean Matrix Root Computation

Warnow, Tandy, Zhu, Binhai

Year:

2003

Language:

english

File:

PDF, 585 KB

english, 2003

50

Hen's Teeth and Whale's Feet: Generalized Characters and Their Compatibility

BENHAM, CRAIG, KANNAN, SAMPATH, PATERSON, MICHAEL, WARNOW, TANDY

Journal:

Journal of Computational Biology

Year:

1995

Language:

english

File:

PDF, 1.27 MB

english, 1995

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