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Bioinformatics (Oxford, England)|November 18, 2021
MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequencesChengze Shen, Paul Zaharias, Tandy WarnowBioinformatics (Oxford, England)|June 27, 2022
Quintet Rooting: rooting species trees under the multi-species coalescent modelYasamin Tabatabaee, Kowshika Sarker, Tandy WarnowJournal of Computational Biology : a Journal of Computational Molecular Cell Biology|November 1, 2011
Algorithms for MDC-based multi-locus phylogeny inference: beyond rooted binary gene trees on single allelesYun Yu, Tandy Warnow, Luay NakhlehMethods in Molecular Biology (Clifton, N.J.)|April 29, 2026
Phylogenetic Placement Using SCAMPP and Batch-SCAMPPEleanor Wedell, Chengze Shen, Tandy WarnowIEEE Transactions on Computational Biology and Bioinformatics|August 14, 2025
BSCAMPP: Batch-Scaled Phylogenetic Placement on Large TreesEleanor Wedell, Chengze Shen, Tandy WarnowBMC Genomics|January 10, 2015
BBCA: Improving the scalability of *BEAST using random binningThéo Zimmermann, Siavash Mirarab, Tandy WarnowSystematic Biology|October 18, 2018
Evaluating Statistical Multiple Sequence Alignment in Comparison to Other Alignment Methods on Protein Data SetsMichael Nute, Ehsan Saleh, Tandy WarnowSystematic Biology|September 25, 2018
Long-Branch Attraction in Species Tree Estimation: Inconsistency of Partitioned Likelihood and Topology-Based Summary MethodsSebastien Roch, Michael Nute, Tandy WarnowAlgorithms for Molecular Biology : AMB|January 28, 2012
MRL and SuperFine+MRL: new supertree methodsNam Nguyen, Siavash Mirarab, Tandy WarnowMethods in Enzymology|May 4, 2005
Advances in phylogeny reconstruction from gene order and content dataBernard M E Moret, Tandy WarnowPageof 14