TY - JOUR AU - Theobald, D. L. PY - 2010 DA - 2010// TI - A formal test of the theory of universal common ancestry JO - Nature VL - 465 UR - https://doi.org/10.1038/nature09014 DO - 10.1038/nature09014 ID - Theobald2010 ER - TY - JOUR AU - de Oliveira Martins, L. AU - Posada, D. PY - 2014 DA - 2014// TI - Testing for universal common ancestry JO - Syst Biol VL - 63 UR - https://doi.org/10.1093/sysbio/syu041 DO - 10.1093/sysbio/syu041 ID - de Oliveira Martins2014 ER - TY - JOUR AU - Koonin, E. V. AU - Wolf, Y. I. PY - 2010 DA - 2010// TI - The common ancestry of life JO - Biol Direct VL - 5 UR - https://doi.org/10.1186/1745-6150-5-64 DO - 10.1186/1745-6150-5-64 ID - Koonin2010 ER - TY - JOUR AU - Yonezawa, T. AU - Hasegawa, M. PY - 2010 DA - 2010// TI - Was the universal common ancestry proved? JO - Nature VL - 468 UR - https://doi.org/10.1038/nature09482 DO - 10.1038/nature09482 ID - Yonezawa2010 ER - TY - JOUR AU - Yonezawa, T. AU - Hasegawa, M. PY - 2012 DA - 2012// TI - Some problems in proving the existence of the universal common ancestor of life on Earth JO - Sci World J VL - 2012 UR - https://doi.org/10.1100/2012/479824 DO - 10.1100/2012/479824 ID - Yonezawa2012 ER - TY - JOUR AU - de Oliveira Martins, L. AU - Posada, D. PY - 2012 DA - 2012// TI - Proving universal common ancestry with similar sequences JO - Trends Evol Biol VL - 4 UR - https://doi.org/10.4081/eb.2012.e5 DO - 10.4081/eb.2012.e5 ID - de Oliveira Martins2012 ER - TY - JOUR AU - Theobald, D. L. PY - 2011 DA - 2011// TI - On universal common ancestry, sequence similarity, and phylogenetic structure: The sins of P-values and the virtues of Bayesian evidence JO - Biol Direct VL - 6 UR - https://doi.org/10.1186/1745-6150-6-60 DO - 10.1186/1745-6150-6-60 ID - Theobald2011 ER - TY - JOUR AU - Lartillot, N. AU - Philippe, H. PY - 2004 DA - 2004// TI - A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process JO - Mol Biol Evol VL - 21 UR - https://doi.org/10.1093/molbev/msh112 DO - 10.1093/molbev/msh112 ID - Lartillot2004 ER - TY - JOUR AU - Quang, L. S. AU - Gascuel, O. AU - Lartillot, N. PY - 2008 DA - 2008// TI - Empirical profile mixture models for phylogenetic reconstruction JO - Bioinformatics (Oxford, England) VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn445 DO - 10.1093/bioinformatics/btn445 ID - Quang2008 ER - TY - JOUR AU - Felsenstein, J. PY - 1981 DA - 1981// TI - Evolutionary trees from DNA sequences: a maximum likelihood approach JO - J Mol Evol VL - 17 UR - https://doi.org/10.1007/BF01734359 DO - 10.1007/BF01734359 ID - Felsenstein1981 ER - TY - JOUR AU - Bruno, W. J. PY - 1996 DA - 1996// TI - Modeling residue usage in aligned protein sequences via maximum likelihood JO - Mol Biol Evol VL - 13 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025583 DO - 10.1093/oxfordjournals.molbev.a025583 ID - Bruno1996 ER - TY - JOUR AU - White, W. T. J. AU - Zhong, B. AU - Penny, D. PY - 2013 DA - 2013// TI - Beyond reasonable doubt: Evolution from dna sequences JO - PLoS ONE VL - 8 UR - https://doi.org/10.1371/journal.pone.0069924 DO - 10.1371/journal.pone.0069924 ID - White2013 ER - TY - JOUR AU - Fletcher, W. AU - Yang, Z. PY - 2009 DA - 2009// TI - INDELible: a flexible simulator of biological sequence evolution JO - Mol Biol Evol VL - 26 UR - https://doi.org/10.1093/molbev/msp098 DO - 10.1093/molbev/msp098 ID - Fletcher2009 ER - TY - BOOK AU - Burnham, K. P. AU - Anderson, D. R. PY - 2002 DA - 2002// TI - (eds.) Model selection and multi–model inference: a practical information-theoretic approach. PB - Springer–Verlag CY - New York, NY, USA ID - Burnham2002 ER - TY - JOUR AU - Burnham, K. P. AU - Anderson, D. P. PY - 2004 DA - 2004// TI - Multimodel inference: understanding AIC and BIC in model selection JO - Sociol Methods Res VL - 33 UR - https://doi.org/10.1177/0049124104268644 DO - 10.1177/0049124104268644 ID - Burnham2004 ER - TY - JOUR AU - Webb, B. -. J. M. AU - Liu, J. S. AU - Lawrence, C. E. PY - 2002 DA - 2002// TI - BALSA: Bayesian algorithm for local sequence alignment JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.5.1268 DO - 10.1093/nar/30.5.1268 ID - Webb2002 ER - TY - JOUR AU - Hendy, M. AU - Penny, D. PY - 1989 DA - 1989// TI - A framework for the quantitative study of evolutionary trees JO - Syst Biol VL - 38 ID - Hendy1989 ER - TY - JOUR AU - Bryant, D. PY - 2009 DA - 2009// TI - Hadamard phylogenetic methods and the n-taxon process JO - Bull Math Biol VL - 71 UR - https://doi.org/10.1007/s11538-008-9364-8 DO - 10.1007/s11538-008-9364-8 ID - Bryant2009 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: multiple sequence alignment with high accuracy and high throughput JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh340 DO - 10.1093/nar/gkh340 ID - Edgar2004 ER - TY - JOUR AU - Faith, D. P. AU - Cranston, P. S. PY - 1991 DA - 1991// TI - Could a cladogram this short have arisen by chance alone?: on permutation tests for cladistic structure JO - Cladistics VL - 7 UR - https://doi.org/10.1111/j.1096-0031.1991.tb00020.x DO - 10.1111/j.1096-0031.1991.tb00020.x ID - Faith1991 ER - TY - JOUR AU - Swofford, D. L. AU - Thorne, J. L. AU - Felsenstein, J. AU - Wiegmann, B. M. PY - 1996 DA - 1996// TI - The topology-dependent permutation test for monophyly does not test for monophyly JO - Syst Biol VL - 45 UR - https://doi.org/10.1093/sysbio/45.4.575 DO - 10.1093/sysbio/45.4.575 ID - Swofford1996 ER - TY - JOUR AU - Guindon, S. AU - Dufayard, J. F. AU - Lefort, V. AU - Anisimova, M. AU - Hordijk, W. AU - Gascuel, O. PY - 2010 DA - 2010// TI - New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of phyml 3.0 JO - Syst Biol VL - 59 UR - https://doi.org/10.1093/sysbio/syq010 DO - 10.1093/sysbio/syq010 ID - Guindon2010 ER - TY - JOUR AU - Darriba, D. AU - Taboada, G. L. AU - Doallo, R. AU - Posada, D. PY - 2011 DA - 2011// TI - ProtTest 3: fast selection of best-fit models of protein evolution JO - Bioinformatics (Oxford, England) VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr088 DO - 10.1093/bioinformatics/btr088 ID - Darriba2011 ER - TY - JOUR AU - Le, S. Q. AU - Gascuel, O. PY - 2008 DA - 2008// TI - An improved general amino acid replacement matrix JO - Mol Biol Evol VL - 25 UR - https://doi.org/10.1093/molbev/msn067 DO - 10.1093/molbev/msn067 ID - Le2008 ER - TY - JOUR AU - Wilkinson, M. AU - Peres-Neto, P. R. AU - Foster, P. G. AU - Moncrieff, C. B. PY - 2002 DA - 2002// TI - Type 1 error rates of the parsimony permutation tail probability test JO - Syst Biol VL - 51 UR - https://doi.org/10.1080/10635150290069931 DO - 10.1080/10635150290069931 ID - Wilkinson2002 ER - TY - JOUR AU - Thorne, J. L. AU - Kishino, H. AU - Felsenstein, J. PY - 1992 DA - 1992// TI - Inching toward reality: an improved likelihood model of sequence evolution JO - J Mol Evol VL - 34 UR - https://doi.org/10.1007/BF00163848 DO - 10.1007/BF00163848 ID - Thorne1992 ER - TY - JOUR AU - Posada, D. AU - Buckley, T. R. PY - 2004 DA - 2004// TI - Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests JO - Syst Biol VL - 53 UR - https://doi.org/10.1080/10635150490522304 DO - 10.1080/10635150490522304 ID - Posada2004 ER -