| Model selection in phylogenetics J Sullivan, P Joyce Annu. Rev. Ecol. Evol. Syst. 36 (1), 445-466, 2005 | 519 | 2005 |
| Performance-based selection of likelihood models for phylogeny estimation V Minin, Z Abdo, P Joyce, J Sullivan Systematic biology 52 (5), 674-683, 2003 | 475 | 2003 |
| Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics J Sullivan, DL Swofford Journal of Mammalian Evolution 4, 77-86, 1997 | 369 | 1997 |
| Comparative phylogeography of northwestern North America: a synthesis SJ Brunsfeld, J Sullivan, DE Soltis, PS Soltis Special Publication-British Ecological Society 14, 319-340, 2001 | 364 | 2001 |
| Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA. RE Hickson, C Simon, A Cooper, GS Spicer, J Sullivan, D Penny Molecular biology and evolution 13 (1), 150-169, 1996 | 322 | 1996 |
| Phylogeography and Molecular Systematics of the Peromyscus Aztecus Species Group (Rodentia: Muridae) Inferred Using Parsimony and Likelihood J Sullivan, JA Markert, CW Kilpatrick Systematic Biology 46 (3), 426-440, 1997 | 307 | 1997 |
| Investigating the evolutionary history of the Pacific Northwest mesic forest ecosystem: hypothesis testing within a comparative phylogeographic framework BC Cartens, SJ Brunsfeld, JR Demboski, JM Good, J Sullivan Evolution 59 (8), 1639-1652, 2005 | 279 | 2005 |
| Evaluating hypotheses of deuterostome phylogeny and chordate evolution with new LSU and SSU ribosomal DNA data CJ Winchell, J Sullivan, CB Cameron, BJ Swalla, J Mallatt Molecular Biology and Evolution 19 (5), 762-776, 2002 | 268 | 2002 |
| 28S and 18S rDNA sequences support the monophyly of lampreys and hagfishes. J Mallatt, J Sullivan Molecular Biology and Evolution 15 (12), 1706-1718, 1998 | 268 | 1998 |
| Evolution of the mitochondrial cytochrome oxidase II gene in Collembola F Frati, C Simon, J Sullivan, DL Swofford Journal of Molecular Evolution 44, 145-158, 1997 | 261 | 1997 |
| Phylogeny inference based on parsimony and other methods using PAUP* DL Swofford, J Sullivan The phylogenetic handbook: a practical approach to DNA and protein phylogeny …, 2003 | 259 | 2003 |
| Comparative phylogeography of Mesoamerican highland rodents: concerted versus independent response to past climatic fluctuations J Sullivan, E Arellano, DS Rogers The American Naturalist 155 (6), 755-768, 2000 | 242 | 2000 |
| Ancient hybridization and mitochondrial capture between two species of chipmunks JM Good, S Hird, N Reid, JR Demboski, SJ Steppan, TR MARTIN‐NIMS, ... Molecular ecology 17 (5), 1313-1327, 2008 | 216 | 2008 |
| The complete nuclear estrogen receptor family in the rainbow trout: discovery of the novel ERα2 and both ERβ isoforms JJ Nagler, T Cavileer, J Sullivan, DG Cyr, C Rexroad III Gene 392 (1-2), 164-173, 2007 | 209 | 2007 |
| PHYLOGEOGRAPHY OF THE TAILED FROG (ASCAPHUS TRUEI): IMPLICATIONS FOR THE BIOGEOGRAPHY OF THE PACIFIC NORTHWEST M Nielson, K Lohman, J Sullivan Evolution 55 (1), 147-160, 2001 | 206 | 2001 |
| Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated? J Sullivan, DL Swofford Systematic Biology 50 (5), 723-729, 2001 | 200 | 2001 |
| Combining data with different distributions of among-site rate variation J Sullivan Systematic Biology 45 (3), 375-380, 1996 | 197 | 1996 |
| The effect of taxon sampling on estimating rate heterogeneity parameters of maximum-likelihood models J Sullivan, DL Swofford, GJP Naylor Molecular Biology and Evolution 16 (10), 1347-1347, 1999 | 173 | 1999 |
| Among-site rate variation and phylogenetic analysis of 12S rRNA in sigmodontine rodents J Sullivan, KE Holsinger, C Simon Molecular Biology and Evolution 12 (6), 988-1001, 1995 | 166 | 1995 |
| Does choice in model selection affect maximum likelihood analysis? J Ripplinger, J Sullivan Systematic biology 57 (1), 76-85, 2008 | 150 | 2008 |
