TY - BOOK AU - Felsenstein, J. PY - 2003 DA - 2003// TI - Inferring Phylogenies PB - Sinauer Associates CY - Sunderland, Massachusetts ID - Felsenstein2003 ER - TY - JOUR AU - Yang, Z. AU - Rannala, B. PY - 2012 DA - 2012// TI - Molecular phylogenetics: Principles and practice JO - Nat Rev Genet VL - 13 UR - https://doi.org/10.1038/nrg3186 DO - 10.1038/nrg3186 ID - Yang2012 ER - TY - JOUR AU - Fitch, W. M. PY - 1995 DA - 1995// TI - Uses for evolutionary trees JO - Philos Trans R Soc Lond Series B Biol Sci VL - 349 UR - https://doi.org/10.1098/rstb.1995.0095 DO - 10.1098/rstb.1995.0095 ID - Fitch1995 ER - TY - JOUR AU - Cavalli-Sforza, L. L. AU - Feldman, M. W. PY - 2003 DA - 2003// TI - The application of molecular genetic approaches to the study of human evolution JO - Nat Genet VL - 33 UR - https://doi.org/10.1038/ng1113 DO - 10.1038/ng1113 ID - Cavalli-Sforza2003 ER - TY - JOUR AU - Holden, C. AU - Mace, R. PY - 2009 DA - 2009// TI - Phylogenetic analysis of the evolution of lactose digestion in adults JO - Hum Biol VL - 81 UR - https://doi.org/10.3378/027.081.0609 DO - 10.3378/027.081.0609 ID - Holden2009 ER - TY - JOUR AU - Mooers, A. O. AU - Heard, S. B. PY - 1997 DA - 1997// TI - Inferring evolutionary process from phylogenetic tree shape JO - Q Rev Biol VL - 72 UR - https://doi.org/10.1086/419657 DO - 10.1086/419657 ID - Mooers1997 ER - TY - BOOK AU - Grumberg, O. AU - Veith, H. PY - 2008 DA - 2008// TI - 25 Years of model checking: history, achievements, perspectives PB - Springer CY - Berlin UR - https://doi.org/10.1007/978-3-540-69850-0 DO - 10.1007/978-3-540-69850-0 ID - Grumberg2008 ER - TY - JOUR AU - Requeno, J. I. AU - Blanco, R. AU - Colom, J. M. PY - 2013 DA - 2013// TI - Temporal logics for phylogenetic analysis via model checking JO - IEEE/ACM Trans Comput Biol Bioinform VL - 10 UR - https://doi.org/10.1109/TCBB.2013.87 DO - 10.1109/TCBB.2013.87 ID - Requeno2013 ER - TY - STD TI - Requeno JI. Formal methods applied to the analysis of phylogenies: Phylogenetic Model Checking PhD thesis: School of Engineering and Architecture, University of Zaragoza; 2014. ID - ref9 ER - TY - BOOK AU - Baier, C. AU - Katoen, J. -. P. PY - 2008 DA - 2008// TI - Principles of model checking PB - The MIT Press CY - Cambridge, Massachusetts ID - Baier2008 ER - TY - JOUR AU - Clarke, E. M. AU - Emerson, E. A. AU - Sistla, A. P. PY - 1986 DA - 1986// TI - Automatic verification of finite-state concurrent systems using temporal logic specifications JO - ACM Trans Program Lang Syst (TOPLAS) VL - 8 UR - https://doi.org/10.1145/5397.5399 DO - 10.1145/5397.5399 ID - Clarke1986 ER - TY - JOUR AU - Requeno, J. I. AU - Colom, J. M. PY - 2014 DA - 2014// TI - Analyzing phylogenetic trees with timed and probabilistic model checking: The lactose persistence case study JO - J Integr Bioinform VL - 11 ID - Requeno2014 ER - TY - JOUR AU - Hansson, H. AU - Jonsson, B. PY - 1994 DA - 1994// TI - A logic for reasoning about time and reliability JO - Form Asp Comput VL - 6 UR - https://doi.org/10.1007/BF01211866 DO - 10.1007/BF01211866 ID - Hansson1994 ER - TY - JOUR AU - Donatelli, S. AU - Haddad, S. AU - Sproston, J. PY - 2009 DA - 2009// TI - Model checking timed and stochastic properties with CSLTA JO - IEEE Trans Softw Eng VL - 35 UR - https://doi.org/10.1109/TSE.2008.108 DO - 10.1109/TSE.2008.108 ID - Donatelli2009 ER - TY - JOUR AU - Konur, S. PY - 2013 DA - 2013// TI - A survey on temporal logics for specifying and verifying real-time systems JO - Frontiers of Computer Science VL - 7 UR - https://doi.org/10.1007/s11704-013-2195-2 DO - 10.1007/s11704-013-2195-2 ID - Konur2013 ER - TY - STD TI - Lewis P, Holder M, Swofford D. Phycas: software for phylogenetic analysis: Storrs, CT: University of Connecticut; 2008. See www.phycas.org. ID - ref16 ER - TY - JOUR AU - Höhna, S. AU - Heath, T. A. AU - Boussau, B. AU - Landis, M. J. AU - Ronquist, F. AU - Huelsenbeck, J. P. PY - 2014 DA - 2014// TI - Probabilistic graphical model representation in phylogenetics JO - Syst Biol VL - 63 UR - https://doi.org/10.1093/sysbio/syu039 DO - 10.1093/sysbio/syu039 ID - Höhna2014 ER - TY - JOUR AU - Bouckaert, R. AU - Heled, J. AU - Kühnert, D. AU - Vaughan, T. AU - Wu, C. H. AU - Xie, D. AU - Suchard, M. A. AU - Rambaut, A. AU - Drummond, A. J. PY - 2014 DA - 2014// TI - Beast 2: a software platform for bayesian evolutionary analysis JO - PLoS Comput Biol VL - 10 UR - https://doi.org/10.1371/journal.pcbi.1003537 DO - 10.1371/journal.pcbi.1003537 ID - Bouckaert2014 ER - TY - STD TI - Stadler T. Evolving trees: Models for speciation and extinction in phylogenetics. PhD thesis. 2008. ID - ref19 ER - TY - JOUR AU - Steel, M. AU - McKenzie, A. PY - 2001 DA - 2001// TI - Properties of phylogenetic trees generated by Yule-type speciation models JO - Math Biosci VL - 170 UR - https://doi.org/10.1016/S0025-5564(00)00061-4 DO - 10.1016/S0025-5564(00)00061-4 ID - Steel2001 ER - TY - JOUR AU - Fitch, W. M. PY - 1971 DA - 1971// TI - Toward defining the course of evolution: Minimum change for a specific tree topology JO - Syst Biol VL - 20 UR - https://doi.org/10.1093/sysbio/20.4.406 DO - 10.1093/sysbio/20.4.406 ID - Fitch1971 ER - TY - JOUR AU - Stamatakis, A. P. AU - Ludwig, T. AU - Meier, H. PY - 2005 DA - 2005// TI - RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti191 DO - 10.1093/bioinformatics/bti191 ID - Stamatakis2005 ER - TY - JOUR PY - 2014 DA - 2014// TI - RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu033 DO - 10.1093/bioinformatics/btu033 ID - ref23 ER - TY - BOOK AU - Yang, Z. PY - 2006 DA - 2006// TI - Computational molecular evolution PB - Oxford University Press CY - New York UR - https://doi.org/10.1093/acprof:oso/9780198567028.001.0001 DO - 10.1093/acprof:oso/9780198567028.001.0001 ID - Yang2006 ER - TY - BOOK AU - Stewart, W. J. PY - 2009 DA - 2009// TI - Probability, Markov chains, queues, and simulation: the mathematical basis of performance modeling PB - Princeton University Press CY - Princeton, New Jersey ID - Stewart2009 ER - TY - CHAP AU - Kwiatkowska, M. AU - Norman, G. AU - Parker, D. ED - Bernardo, M. ED - Hillston, J. PY - 2007 DA - 2007// TI - Stochastic model checking BT - 7th International School on Formal Methods for Performance Evaluation. LNCS PB - Springer CY - Berlin ID - Kwiatkowska2007 ER - TY - BOOK AU - Clarke, E. M. AU - Grumberg, O. AU - Peled, D. A. PY - 2000 DA - 2000// TI - Model checking PB - The MIT Press CY - Cambridge, Massachusetts ID - Clarke2000 ER - TY - JOUR AU - Montoya, J. AU - López-Gallardo, E. AU - Díez-Sánchez, C. AU - López-Pérez, M. J. AU - Ruiz-Pesini, E. PY - 2009 DA - 2009// TI - 20 years of human mtDNA pathologic point mutations: Carefully reading the pathogenicity criteria JO - Biochimica et Biophysica Acta VL - 1787 UR - https://doi.org/10.1016/j.bbabio.2008.09.003 DO - 10.1016/j.bbabio.2008.09.003 ID - Montoya2009 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 - Lio, P. AU - Goldman, N. PY - 1998 DA - 1998// TI - Models of molecular evolution and phylogeny JO - Genome Res VL - 8 ID - Lio1998 ER - TY - STD TI - Cho A. Constructing phylogenetic trees using maximum likelihood. PhD thesis, Scripps Senior These. 2012. ID - ref31 ER - TY - BOOK AU - Wägele, J. -. W. PY - 2005 DA - 2005// TI - Foundations of phylogenetic systematics PB - Pfeil CY - Münich ID - Wägele2005 ER - TY - JOUR AU - Tuffley, C. AU - Steel, M. PY - 1997 DA - 1997// TI - Links between maximum likelihood and maximum parsimony under a simple model of site substitution JO - Bull Math Biol VL - 59 UR - https://doi.org/10.1007/BF02459467 DO - 10.1007/BF02459467 ID - Tuffley1997 ER - TY - CHAP AU - Jansen, D. N. AU - Katoen, J. -. P. AU - Oldenkamp, M. AU - Stoelinga, M. AU - Zapreev, I. ED - Yorav, K. PY - 2008 DA - 2008// TI - How fast and fat is your probabilistic model checker? An experimental performance comparison BT - Proceedings 3rd International Haifa Verification Conference on Hardware and Software, Verification and Testing. LNCS PB - Springer CY - Berlin ID - Jansen2008 ER - TY - CHAP ED - Gopalakrishnan, G. ED - Qadeer, S. PY - 2011 DA - 2011// TI - PRISM 4.0: Verification of probabilistic real-time systems BT - Proceedings 23rd International Conference on Computer Aided Verification. LNCS PB - Springer CY - Berlin ID - ref35 ER - TY - STD TI - Katoen JP, Khattri M, Zapreev IS. A markov reward model checker. In: Proceedings 2nd International Conference on the Quantitative Evaluation of Systems. IEEE: 2005. p. 243–244, doi:10.1109/QEST.2005.2. ID - ref36 ER - TY - STD TI - Mateescu R, Requeno JI. On-the-fly model checking for extended action-based probabilistic operators In: Bošnački D, Wijs A, editors. 23rd International SPIN Symposium on Model Checking of Software. Springer: 2016. vol. 9641 p. 189–207. ID - ref37 ER - TY - JOUR AU - Stamatakis, A. P. AU - Ludwig, T. AU - Meier, H. PY - 2004 DA - 2004// TI - The AxML program family for maximum likelihood-based phylogenetic tree inference JO - Concurr Comput Pract Experience VL - 16 UR - https://doi.org/10.1002/cpe.817 DO - 10.1002/cpe.817 ID - Stamatakis2004 ER - TY - JOUR AU - Darriba, D. AU - Taboada, G. L. AU - Doallo, R. AU - Posada, D. PY - 2012 DA - 2012// TI - jModelTest 2: More models, new heuristics and parallel computing JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.2109 DO - 10.1038/nmeth.2109 ID - Darriba2012 ER - TY - JOUR AU - Stajich, J. E. AU - Block, D. AU - Boulez, K. AU - Brenner, S. E. AU - Chervitz, S. A. AU - Dagdigian, C. AU - Fuellen, G. AU - Gilbert, J. G. R. AU - Korf, I. AU - Lapp, H. PY - 2002 DA - 2002// TI - The Bioperl toolkit: Perl modules for the life sciences JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.361602 DO - 10.1101/gr.361602 ID - Stajich2002 ER -