Contemporaneous radiations of fungi and plants linked to symbiosis von Lutzoni, François, Nowak, Michael D., Alfaro, Michael E., Reeb, Valérie, Miadlikowska, Jolanta, Krug, Michael, Arnold, A. Elizabeth, Lewis, Louise A., Swofford, David L., Hibbett, David, Hilu, Khidir, James, Timothy Y., Quandt, Dietmar, Magallón, Susana

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AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics von Nylander, Johan A.A., Wilgenbusch, James C., Warren, Dan L., Swofford, David L.

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BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics von Ayres, Daniel L, Darling, Aaron, Zwickl, Derrick J, Beerli, Peter, Holder, Mark T, Lewis, Paul O, Huelsenbeck, John P, Ronquist, Fredrik, Swofford, David L, Cummings, Michael P, Rambaut, Andrew, Suchard, Marc A

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Estimation of speciation times under the multispecies coalescent von Peng, Jing, Swofford, David L, Kubatko, Laura

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BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics von Ayres, Daniel L., Cummings, Michael P., Baele, Guy, Darling, Aaron E., Lewis, Paul O., Swofford, David L., Huelsenbeck, John P., Lemey, Philippe, Rambaut, Andrew, Suchard, Marc A.

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Inference of Phylogenetic Networks from Sequence Data using Composite Likelihood von Kong, Sungsik, Swofford, David L, Kubatko, Laura S

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Bias in Phylogenetic Estimation and Its Relevance to the Choice between Parsimony and Likelihood Methods von Swofford, David L., Waddell, Peter J., Huelsenbeck, John P., Foster, Peter G., Lewis, Paul O., Rogers, James S., Olmstead, R.

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Phylogeny of the manta and devilrays (Chondrichthyes: mobulidae), with an updated taxonomic arrangement for the family von White, William T, Corrigan, Shannon, Yang, Lei, Henderson, Aaron C, Bazinet, Adam L, Swofford, David L, Naylor, Gavin J P

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Are Guinea Pigs Rodents? The Importance of Adequate Models in Molecular Phylogenetics von Sullivan, Jack, Swofford, David L

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Geogenetic patterns in mouse lemurs (genus Microcebus) reveal the ghosts of Madagascar’s forests past von Yoder, Anne D., Campbell, C. Ryan, Blanco, Marina B., dos Reis, Mario, Ganzhorn, Jörg U., Goodman, Steven M., Hunnicutt, Kelsie E., Larsen, Peter A., Kappeler, Peter M., Rasoloarison, Rodin M., Ralison, José M., Swofford, David L., Weisrock, David W.

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Phycas: Software for Bayesian Phylogenetic Analysis von Lewis, Paul O., Holder, Mark T., Swofford, David L.

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Natural Hybridization between Genera That Diverged from Each Other Approximately 60 Million Years Ago von Rothfels, Carl J., Johnson, Anne K., Hovenkamp, Peter H., Swofford, David L., Roskam, Harry C., Fraser-Jenkins, Christopher R., Windham, Michael D., Pryer, Kathleen M.

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Evolution of the mitochondrial cytochrome oxidase II gene in collembola von Frati, F, Simon, C, Sullivan, J, Swofford, D L

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Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA von Anderson, Frank E., Swofford, David L.

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Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation von Sullivan, Jack, Abdo, Zaid, Joyce, Paul, Swofford, David L

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Bias in Phylogenetic Estimation and Its Relevance to the Choice between Parsimony and Likelihood Methods von Swofford, David L., Waddell, Peter J., Huelsenbeck, John P., Foster, Peter G., Lewis, Paul O., Rogers, James S.

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Taxon sampling revisited von Poe, Steven, Swofford, David L

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The Akaike Information Criterion Will Not Choose the No Common Mechanism Model von Holder, Mark T., Lewis, Paul O., Swofford, David L., Gascuel, Olivier

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Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus von Horvath, Julie E, Sheedy, Christina B, Merrett, Stephanie L, Diallo, Abdoulaye Banire, Swofford, David L, NISC Comparative Sequencing Program, Green, Eric D, Willard, Huntington F

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Partitioning and Combining Data in Phylogenetic Analysis von Bull, J. J., Huelsenbeck, John P., Cunningham, Clifford W., Swofford, David L., Waddell, Peter J.

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