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Authors: Tandy Warnow
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Journal Article

Phylogenomic branch length estimation using quartets

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Yasamin Tabatabaee and others
Bioinformatics, Volume 39, Issue Supplement_1, June 2023, Pages i185–i193, https://doi.org/10.1093/bioinformatics/btad221
Published: 30 June 2023
Journal Article

UPP2: fast and accurate alignment of datasets with fragmentary sequences

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Minhyuk Park and others
Bioinformatics, Volume 39, Issue 1, January 2023, btad007, https://doi.org/10.1093/bioinformatics/btad007
Published: 10 January 2023
Journal Article

Quintet Rooting: rooting species trees under the multi-species coalescent model

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Yasamin Tabatabaee and others
Bioinformatics, Volume 38, Issue Supplement_1, July 2022, Pages i109–i117, https://doi.org/10.1093/bioinformatics/btac224
Published: 27 June 2022
Journal Article

MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences

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Chengze Shen and others
Bioinformatics, Volume 38, Issue 4, February 2022, Pages 918–924, https://doi.org/10.1093/bioinformatics/btab788
Published: 17 November 2021
Journal Article

Accurate large-scale phylogeny-aware alignment using BAli-Phy

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Maya Gupta and others
Bioinformatics, Volume 37, Issue 24, December 2021, Pages 4677–4683, https://doi.org/10.1093/bioinformatics/btab555
Published: 28 July 2021
Journal Article

FASTRAL: improving scalability of phylogenomic analysis

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Payam Dibaeinia and others
Bioinformatics, Volume 37, Issue 16, August 2021, Pages 2317–2324, https://doi.org/10.1093/bioinformatics/btab093
Published: 08 February 2021
Journal Article

TIPP2: metagenomic taxonomic profiling using phylogenetic markers

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Nidhi Shah and others
Bioinformatics, Volume 37, Issue 13, July 2021, Pages 1839–1845, https://doi.org/10.1093/bioinformatics/btab023
Published: 20 January 2021
Journal Article

MAGUS: Multiple sequence Alignment using Graph clUStering

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Vladimir Smirnov and Tandy Warnow
Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1666–1672, https://doi.org/10.1093/bioinformatics/btaa992
Published: 30 November 2020
Journal Article

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

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Erin K Molloy and Tandy Warnow
Bioinformatics, Volume 36, Issue Supplement_1, July 2020, Pages i57–i65, https://doi.org/10.1093/bioinformatics/btaa444
Published: 13 July 2020
Journal Article

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

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Erin K Molloy and Tandy Warnow
Bioinformatics, Volume 35, Issue 14, July 2019, Pages i417–i426, https://doi.org/10.1093/bioinformatics/btz344
Published: 05 July 2019
Journal Article

Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows

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Nidhi Shah and others
Bioinformatics, Volume 35, Issue 9, May 2019, Pages 1613–1614, https://doi.org/10.1093/bioinformatics/bty833
Published: 24 September 2018
Journal Article

PASTA for proteins

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Kodi Collins and Tandy Warnow
Bioinformatics, Volume 34, Issue 22, November 2018, Pages 3939–3941, https://doi.org/10.1093/bioinformatics/bty495
Published: 19 June 2018
Journal Article

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

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Pranjal Vachaspati and Tandy Warnow
Bioinformatics, Volume 33, Issue 5, March 2017, Pages 631–639, https://doi.org/10.1093/bioinformatics/btw600
Published: 23 September 2016
Journal Article

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

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Siavash Mirarab and Tandy Warnow
Bioinformatics, Volume 31, Issue 12, June 2015, Pages i44–i52, https://doi.org/10.1093/bioinformatics/btv234
Published: 10 June 2015
Journal Article

TIPP: taxonomic identification and phylogenetic profiling

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Nam-phuong Nguyen and others
Bioinformatics, Volume 30, Issue 24, December 2014, Pages 3548–3555, https://doi.org/10.1093/bioinformatics/btu721
Published: 29 October 2014
Journal Article

Naive binning improves phylogenomic analyses

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Md Shamsuzzoha Bayzid and Tandy Warnow
Bioinformatics, Volume 29, Issue 18, September 2013, Pages 2277–2284, https://doi.org/10.1093/bioinformatics/btt394
Published: 09 July 2013
Journal Article

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

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Serita Nelesen and others
Bioinformatics, Volume 28, Issue 12, June 2012, Pages i274–i282, https://doi.org/10.1093/bioinformatics/bts218
Published: 09 June 2012
Journal Article

FASTSP: linear time calculation of alignment accuracy

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Siavash Mirarab and Tandy Warnow
Bioinformatics, Volume 27, Issue 23, December 2011, Pages 3250–3258, https://doi.org/10.1093/bioinformatics/btr553
Published: 07 October 2011
Journal Article

Statistically based postprocessing of phylogenetic analysis by clustering

Cara Stockham and others
Bioinformatics, Volume 18, Issue suppl_1, July 2002, Pages S285–S293, https://doi.org/10.1093/bioinformatics/18.suppl_1.S285
Published: 01 July 2002
Journal Article

Designing fast converging phylogenetic methods

Luay Nakhleh and others
Bioinformatics, Volume 17, Issue suppl_1, June 2001, Pages S190–S198, https://doi.org/10.1093/bioinformatics/17.suppl_1.S190
Published: 01 June 2001