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For Methods and theory of phylogenetic inference

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ID	Title	Section	Authors	Keywords
437	Dead Green: Conceptual and Empirical Perspectives on Integrating Fossils and Extant Taxa in Phylogenetic Analysis	Conference Wide	Soltis, Pamela S., Manos, Paul S., Manchester, Steven R., Bell, Charles, Soltis, Douglas E..	divergence time estimates fossils phylogeny reconstruction missing data
174	Estimating speciation and extinction rates from phylogenetic trees: A Markov chain Monte Carlo approach	Conference Wide	Salamin, Nicolas.	birth and death speciation and extinction rates Markov chain Monte Carlo importance sampling macroevolution phylogenetics
132	Evaluating partitioned models for phylogenetic analysis of combined data.	Conference Wide	Kelchner, Scot A., Swofford, David L., Wilgenbusch, James.	phylogenetic inference systematic error simulation outgroup rooting partitioned models combined data
123	Incongruence around the species level: Is the glass half full or half empty?	Conference Wide	Doyle, Jeff J..	incongruence gene tree/species tree tokogeny
761	King Kong versus Godzilla: supertree and supermatrix phylogenetics	Conference Wide	Sanderson, MJ, Driskell, Amy.	genomics supertree supermatrix database mining
154	Methods and theory of phylogenetic inference	Conference Wide	Kelchner, Scot A., Simmons, Mark P..
56	(Mis)rooting phylogenetic trees	Conference Wide	Graham, Sean W..	trees phylogenetic inference systematic error long-branch attraction rooting Tree of Life outgroup ingroup root node
528	Parsimony vs. Bayesian likelihood for phylogenetic inference from heterogeneous datasets	Conference Wide	Simmons, Mark P., Zhang, Li-Bing, Webb, Colleen T., Reeves, Aaron, Miller, Jeremy A..	rate heterogeneity phylogenetic inference Bayesian likelihood parsimony branch support simulations
712	Resampling branch support strategies: balancing accuracy and effort	Conference Wide	Freudenstein, John.	branch support cladistic analysis jackknife
36	The influence of flat topological priors on Bayesian inference of phylogenetics	Conference Wide	Randle, Christopher P., Pickett, Kurt M..	Bayesian phylogenetics bootstrap jackknife clade posterior probability prior probability
509	The limits of conventional cladistic analysis - the 500-terminal rbcL matrix, sources of variation in the estimation of branch support, and some gentle criticisms of supertree methods	Conference Wide	Davis, Jerrold I., Nixon, Kevin C., Little, Damon P..	rbcL cladistic analysis supertree zilla bootstrap jackknife
432	The use of ESTs in phylogenetic analyses	Conference Wide	Soltis, Douglas E., Soltis, Pamela S., Albert, Victor A., Kim, Sangtae.	expressed sequence tags phylogeny reconstruction genomic resources
308	The utility of whole chloroplast genome sequencing for reconstructing deep nodes in plants with an example from basal angiosperms	Conference Wide	Jansen, Robert K., dePamphilis, Claude W., Raubeson, Linda, Leebens-Mack, James, McNeal, Joel R., Cui, Liying, Zhang, Yan, Wyman, Stacia, Boore, Jeffrey, Kuehl, Jennifer.	Amborella basal angiosperms chloroplast DNA comparative genomics genomics phylogenetics seed plants