David Swofford, Ph.D. - Publications

Affiliations: 
Biology Duke University, Durham, NC 
Area:
Phylogenetics

37 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Ayres DL, Cummings MP, Baele G, Darling AE, Lewis PO, Swofford DL, Huelsenbeck JP, Lemey P, Rambaut A, Suchard MA. BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics. Systematic Biology. PMID 31034053 DOI: 10.1093/Sysbio/Syz020  1
2016 Yoder AD, Campbell CR, Blanco MB, Dos Reis M, Ganzhorn JU, Goodman SM, Hunnicutt KE, Larsen PA, Kappeler PM, Rasoloarison RM, Ralison JM, Swofford DL, Weisrock DW. Geogenetic patterns in mouse lemurs (genus Microcebus) reveal the ghosts of Madagascar's forests past. Proceedings of the National Academy of Sciences of the United States of America. PMID 27432945 DOI: 10.1073/Pnas.1601081113  1
2015 Rothfels CJ, Johnson AK, Hovenkamp PH, Swofford DL, Roskam HC, Fraser-Jenkins CR, Windham MD, Pryer KM. Natural hybridization between genera that diverged from each other approximately 60 million years ago. The American Naturalist. 185: 433-42. PMID 25674696 DOI: 10.1086/679662  1
2015 Lewis PO, Holder MT, Swofford DL. Phycas: software for Bayesian phylogenetic analysis. Systematic Biology. 64: 525-31. PMID 25577605 DOI: 10.1093/Sysbio/Syu132  1
2012 Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP, Rambaut A, Suchard MA. BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Systematic Biology. 61: 170-3. PMID 21963610 DOI: 10.1093/Sysbio/Syr100  1
2011 Horvath JE, Sheedy CB, Merrett SL, Diallo AB, Swofford DL, NISC Comparative Sequencing Program, Green ED, Willard HF. Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus. Genome Research. 21: 850-62. PMID 21518738 DOI: 10.1101/Gr.111849.110  1
2011 Kurt Lienau E, DeSalle R, Allard M, Brown EW, Swofford D, Rosenfeld JA, Sarkar IN, Planet PJ. The mega-matrix tree of life: Using genome-scale horizontal gene transfer and sequence evolution data as information about the vertical history of life Cladistics. 27: 417-427. DOI: 10.1111/J.1096-0031.2010.00337.X  1
2010 Holder MT, Lewis PO, Swofford DL. The akaike information criterion will not choose the no common mechanism model. Systematic Biology. 59: 477-85. PMID 20547783 DOI: 10.1093/Sysbio/Syq028  1
2008 Min D, Josephine HR, Li H, Lakner C, MacPherson IS, Naylor GJ, Swofford D, Hedstrom L, Yang W. An enzymatic atavist revealed in dual pathways for water activation. Plos Biology. 6: e206. PMID 18752347 DOI: 10.1371/Journal.Pbio.0060206  1
2008 Nylander JA, Wilgenbusch JC, Warren DL, Swofford DL. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics (Oxford, England). 24: 581-3. PMID 17766271 DOI: 10.1093/Bioinformatics/Btm388  1
2005 Holder MT, Lewis PO, Swofford DL, Larget B. Hastings ratio of the LOCAL proposal used in Bayesian phylogenetics. Systematic Biology. 54: 961-5. PMID 16385776 DOI: 10.1080/10635150500354670  1
2005 Sullivan J, Abdo Z, Joyce P, Swofford DL. Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation. Molecular Biology and Evolution. 22: 1386-92. PMID 15758203 DOI: 10.1093/Molbev/Msi129  1
2004 Anderson FE, Swofford DL. Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA. Molecular Phylogenetics and Evolution. 33: 440-51. PMID 15336677 DOI: 10.1016/J.Ympev.2004.06.015  1
2003 Wilgenbusch JC, Swofford D. Inferring evolutionary trees with PAUP*. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 6.4. PMID 18428704 DOI: 10.1002/0471250953.Bi0604S00  1
2002 Kassler TW, Koppelman JB, Near TJ, Dillman CB, Levengood JM, Swofford DL, VanOrman JL, Claussen JE, Philipp DP. Molecular and morphological analyses of the black basses: Implications for taxonomy and conservation American Fisheries Society Symposium. 2002: 291-322.  1
2001 Sullivan J, Swofford DL. 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? Systematic Biology. 50: 723-9. PMID 12116942 DOI: 10.1080/106351501753328848  1
2001 Swofford DL, Waddell PJ, Huelsenbeck JP, Foster PG, Lewis PO, Rogers JS. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Systematic Biology. 50: 525-39. PMID 12116651 DOI: 10.1080/10635150117959  1
2001 Lewis PO, Swofford DL. Back to the future: Bayesian inference arrives in phylogenetics Trends in Ecology and Evolution. 16: 600-601. DOI: 10.1016/S0169-5347(01)02322-9  1
2000 Huelsenbeck JP, Larget B, Swofford D. A compound poisson process for relaxing the molecular clock. Genetics. 154: 1879-92. PMID 10747076  1
1999 Rogers JS, Swofford DL. Multiple local maxima for likelihoods of phylogenetic trees: a simulation study. Molecular Biology and Evolution. 16: 1079-85. PMID 10507922  1
1999 Poe S, Swofford DL. Taxon sampling revisited. Nature. 398: 299-300. PMID 10192331 DOI: 10.1038/18589  1
1999 Sullivan J, Swofford DL, Naylor GJP. The effect of taxon sampling on estimating rate heterogeneity parameters of maximum-likelihood models Molecular Biology and Evolution. 16: 1347-1356. DOI: 10.1093/Oxfordjournals.Molbev.A026045  1
1998 Rogers JS, Swofford DL. A fast method for approximating maximum likelihoods of phylogenetic trees from nucleotide sequences. Systematic Biology. 47: 77-89. PMID 12064242  1
1997 Berlocher SH, Swofford DL. Searching for phylogenetic trees under the frequency parsimony criterion: an approximation using generalized parsimony. Systematic Biology. 46: 211-5. PMID 11975353 DOI: 10.1093/Sysbio/46.1.211  1
1997 Maddison DR, Swofford DL, Maddison WP. NEXUS: an extensible file format for systematic information. Systematic Biology. 46: 590-621. PMID 11975335 DOI: 10.1093/Sysbio/46.4.590  1
1997 Frati F, Simon C, Sullivan J, Swofford DL. Evolution of the mitochondrial cytochrome oxidase II gene in collembola. Journal of Molecular Evolution. 44: 145-58. PMID 9069175 DOI: 10.1007/Pl00006131  1
1997 Sullivan J, Swofford DL. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics Journal of Mammalian Evolution. 4: 77-86. DOI: 10.1023/A:1027314112438  1
1997 Swofford DL, Siddall ME. Uneconomical Diagnosis of Cladograms: Comments on Wheeler and Nixon's Method for Sankoff Optimization Cladistics. 13: 153-159. DOI: 10.1006/Clad.1997.0037  1
1996 Swofford DL, Thorne JL, Felsenstein J, Wiegmann BM. The topology-dependent permutation test for monophyly does not test for monophyly Systematic Biology. 45: 575-579. DOI: 10.1093/Sysbio/45.4.575  1
1994 Hillis DM, Huelsenbeck JP, Swofford DL. Hobgoblin of phylogenetics? Nature. 369: 363-4. PMID 8196763 DOI: 10.1038/369363A0  1
1994 Huelsenbeck JP, Swofford DL, Cunningham CW, Bull JJ, Waddell PJ. Is character weighting a panacea for the problem of data heterogeneity in phylogenetic analysis? Systematic Biology. 43: 288-291. DOI: 10.1093/Sysbio/43.2.288  1
1993 Bull JJ, Huelsenbeck JP, Cunningham CW, Swofford DL, Waddell PJ. Partitioning and combining data in phylogenetic analysis Systematic Biology. 42: 384-397. DOI: 10.1093/Sysbio/42.3.384  1
1992 Maddison DR, Ruvolo M, Swofford DL. Geographic origins of human mitochondrial DNA: Phylogenetic evidence from control region sequences Systematic Biology. 41: 111-124. DOI: 10.1093/Sysbio/41.1.111  1
1991 Stock DW, Swofford DL. Coelacanth's relationships [4] Nature. 353: 217-218. PMID 1896070  1
1987 Swofford DL, Maddison WP. Reconstructing ancestral character states under Wagner parsimony Mathematical Biosciences. 87: 199-229. DOI: 10.1016/0025-5564(87)90074-5  1
1984 Page LM, Swofford DL. Morphological correlates of ecological specialization in darters Environmental Biology of Fishes. 11: 139-159. DOI: 10.1007/BF00002263  1
1981 Swofford DL, Selander RB. BIOSYS-1; a FORTRAN program for the comprehensive analysis of electrophoretic data in population genetics and systematics Journal of Heredity. 72: 281-283.  1
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