TY - JOUR AU - Gabaldon, T. PY - 2008 DA - 2008// TI - Large-scale assignment of orthology: back to phylogenetics? JO - Genome Biol VL - 9 UR - https://doi.org/10.1186/gb-2008-9-10-235 DO - 10.1186/gb-2008-9-10-235 ID - Gabaldon2008 ER - TY - CHAP AU - Li, W. -. H. PY - 1997 DA - 1997// BT - Molecular evolution PB - Sinauer CY - Sunderland, MA. ID - Li1997 ER - TY - JOUR AU - Thorne, J. L. AU - Kishino, H. PY - 2002 DA - 2002// TI - Divergence time and evolutionary rate estimation with multilocus data JO - Syst Biol VL - 51 UR - https://doi.org/10.1080/10635150290102456 DO - 10.1080/10635150290102456 ID - Thorne2002 ER - TY - JOUR AU - Cassens, I. AU - Vicario, S. AU - Waddell, V. G. AU - Balchowsky, H. AU - Van Belle, D. AU - Ding, W. AU - Fan, C. AU - Mohan, R. S. AU - Simoes-Lopes, P. C. AU - Bastida, R. PY - 2000 DA - 2000// TI - Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages JO - Proc Natl Acad Sci USA VL - 97 UR - https://doi.org/10.1073/pnas.97.21.11343 DO - 10.1073/pnas.97.21.11343 ID - Cassens2000 ER - TY - JOUR AU - Thorne, J. L. AU - Kishino, H. AU - Painter, I. S. PY - 1998 DA - 1998// TI - Estimating the rate of evolution of the rate of molecular evolution JO - Molecular Biology and Evolution VL - 15 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025892 DO - 10.1093/oxfordjournals.molbev.a025892 ID - Thorne1998 ER - TY - JOUR AU - Blanchette, M. AU - Green, E. D. AU - Miller, W. AU - Haussler, D. PY - 2004 DA - 2004// TI - Reconstructing large regions of an ancestral mammalian genome in silico JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.2800104 DO - 10.1101/gr.2800104 ID - Blanchette2004 ER - TY - JOUR AU - Chang, B. S. AU - Jonsson, K. AU - Kazmi, M. A. AU - Donoghue, M. J. AU - Sakmar, T. P. PY - 2002 DA - 2002// TI - Recreating a functional ancestral archosaur visual pigment JO - Molecular biology and evolution VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a004211 DO - 10.1093/oxfordjournals.molbev.a004211 ID - Chang2002 ER - TY - JOUR AU - Chang, B. S. AU - Ugalde, J. A. AU - Matz, M. V. PY - 2005 DA - 2005// TI - Applications of ancestral protein reconstruction in understanding protein function: GFP-like proteins JO - Methods Enzymol VL - 395 UR - https://doi.org/10.1016/S0076-6879(05)95034-9 DO - 10.1016/S0076-6879(05)95034-9 ID - Chang2005 ER - TY - JOUR AU - Williams, P. D. AU - Pollock, D. D. AU - Blackburne, B. P. AU - Goldstein, R. A. PY - 2006 DA - 2006// TI - Assessing the accuracy of ancestral protein reconstruction methods JO - PLoS computational biology VL - 2 UR - https://doi.org/10.1371/journal.pcbi.0020069 DO - 10.1371/journal.pcbi.0020069 ID - Williams2006 ER - TY - JOUR AU - Zhang, J. AU - Nielsen, R. AU - Yang, Z. PY - 2005 DA - 2005// TI - Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level JO - Molecular biology and evolution VL - 22 UR - https://doi.org/10.1093/molbev/msi237 DO - 10.1093/molbev/msi237 ID - Zhang2005 ER - TY - JOUR AU - Meegaskumbura, M. AU - Bossuyt, F. AU - Pethiyagoda, R. AU - Manamendra-Arachchi, K. AU - Bahir, M. AU - Milinkovitch, M. C. AU - Schneider, C. J. PY - 2002 DA - 2002// TI - Sri Lanka: an amphibian hot spot JO - Science VL - 298 UR - https://doi.org/10.1126/science.298.5592.379 DO - 10.1126/science.298.5592.379 ID - Meegaskumbura2002 ER - TY - JOUR AU - Springer, M. S. AU - Stanhope, M. J. AU - Madsen, O. AU - de Jong, W. W. PY - 2004 DA - 2004// TI - Molecules consolidate the placental mammal tree JO - Trends in ecology & evolution (Personal edition) VL - 19 UR - https://doi.org/10.1016/j.tree.2004.05.006 DO - 10.1016/j.tree.2004.05.006 ID - Springer2004 ER - TY - JOUR AU - Bossuyt, F. AU - Brown, R. M. AU - Hillis, D. M. AU - Cannatella, D. C. AU - Milinkovitch, M. C. PY - 2006 DA - 2006// TI - Phylogeny and biogeography of a cosmopolitan frog radiation: Late cretaceous diversification resulted in continent-scale endemism in the family ranidae JO - Syst Biol VL - 55 UR - https://doi.org/10.1080/10635150600812551 DO - 10.1080/10635150600812551 ID - Bossuyt2006 ER - TY - JOUR AU - Graham, R. L. AU - Foulds, L. R. PY - 1982 DA - 1982// TI - Unlikelihood that Minimal Phylogenies for a Realistic Biological Study Can Be Constructed in Reasonable Computational Time JO - Math Bioscience VL - 60 UR - https://doi.org/10.1016/0025-5564(82)90125-0 DO - 10.1016/0025-5564(82)90125-0 ID - Graham1982 ER - TY - JOUR AU - Chor, B. AU - Tuller, T. PY - 2005 DA - 2005// TI - Maximum likelihood of evolutionary trees: hardness and approximation JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti1027 DO - 10.1093/bioinformatics/bti1027 ID - Chor2005 ER - TY - JOUR AU - Felsenstein, J. PY - 1981 DA - 1981// TI - Evolutionary trees from DNA sequences: a maximum likelihood approach JO - Journal of molecular evolution VL - 17 UR - https://doi.org/10.1007/BF01734359 DO - 10.1007/BF01734359 ID - Felsenstein1981 ER - TY - CHAP AU - Felsenstein, J. PY - 2004 DA - 2004// BT - Inferring Phylogenies PB - Sinauer Associates Inc CY - Sunderland ID - Felsenstein2004 ER - TY - JOUR AU - Swofford, D. L. AU - Waddell, P. J. AU - Huelsenbeck, J. P. AU - Foster, P. G. AU - Lewis, P. O. AU - Rogers, J. S. PY - 2001 DA - 2001// TI - Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods JO - Syst Biol VL - 50 UR - https://doi.org/10.1080/106351501750435086 DO - 10.1080/106351501750435086 ID - Swofford2001 ER - TY - JOUR AU - Holder, M. AU - Lewis, P. O. PY - 2003 DA - 2003// TI - Phylogeny estimation: traditional and Bayesian approaches JO - Nat Rev Genet VL - 4 UR - https://doi.org/10.1038/nrg1044 DO - 10.1038/nrg1044 ID - Holder2003 ER - TY - JOUR AU - Huelsenbeck, J. P. AU - Larget, B. AU - Miller, R. E. AU - Ronquist, F. PY - 2002 DA - 2002// TI - Potential applications and pitfalls of Bayesian inference of phylogeny JO - Syst Biol VL - 51 UR - https://doi.org/10.1080/10635150290102366 DO - 10.1080/10635150290102366 ID - Huelsenbeck2002 ER - TY - JOUR AU - Salter, L. A. AU - Pearl, D. K. PY - 2001 DA - 2001// TI - Stochastic search strategy for estimation of maximum likelihood phylogenetic trees JO - Syst Biol VL - 50 UR - https://doi.org/10.1080/106351501750107413 DO - 10.1080/106351501750107413 ID - Salter2001 ER - TY - JOUR AU - Katoh, K. AU - Kuma, K. AU - Miyata, T. PY - 2001 DA - 2001// TI - Genetic algorithm-based maximum-likelihood analysis for molecular phylogeny JO - J Mol Evol VL - 53 UR - https://doi.org/10.1007/s002390010238 DO - 10.1007/s002390010238 ID - Katoh2001 ER - TY - JOUR AU - Lemmon, A. R. AU - Milinkovitch, M. C. PY - 2002 DA - 2002// TI - The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation JO - Proc Natl Acad Sci USA VL - 99 UR - https://doi.org/10.1073/pnas.162224399 DO - 10.1073/pnas.162224399 ID - Lemmon2002 ER - TY - JOUR AU - Lewis, P. O. PY - 1998 DA - 1998// TI - A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data JO - Mol biol evol VL - 15 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025924 DO - 10.1093/oxfordjournals.molbev.a025924 ID - Lewis1998 ER - TY - CHAP AU - Matsuda, H. PY - 1996 DA - 1996// TI - Protein phylogenetic inference using maximum likelihood with a genetic algorithm BT - Pacific symposium on biocomputing '96 PB - World Scientific CY - London ID - Matsuda1996 ER - TY - CHAP AU - Zwickl, D. J. PY - 2006 DA - 2006// BT - Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion PB - The University of Texas CY - Austin, Tx, USA. ID - Zwickl2006 ER - TY - JOUR AU - Ronquist, F. AU - Huelsenbeck, J. P. PY - 2003 DA - 2003// TI - MrBayes 3: Bayesian phylogenetic inference under mixed models JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg180 DO - 10.1093/bioinformatics/btg180 ID - Ronquist2003 ER - TY - JOUR AU - Stamatakis, A. PY - 2006 DA - 2006// TI - RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl446 DO - 10.1093/bioinformatics/btl446 ID - Stamatakis2006 ER - TY - JOUR AU - Suchard, M. A. AU - Rambaut, A. PY - 2009 DA - 2009// TI - Many-core algorithms for statistical phylogenetics JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp244 DO - 10.1093/bioinformatics/btp244 ID - Suchard2009 ER - TY - JOUR AU - Tavaré, S. PY - 1986 DA - 1986// TI - Some Probabilistic and Statistical Problems in the Analysis of DNA Sequences JO - American Mathematical Society: Lectures on Mathematics in the Life Sciences VL - 17 ID - Tavaré1986 ER - TY - JOUR AU - Yang, Z. PY - 1994 DA - 1994// TI - Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods JO - J Mol Evol VL - 39 UR - https://doi.org/10.1007/BF00160154 DO - 10.1007/BF00160154 ID - Yang1994 ER - TY - JOUR AU - Yang, Z. PY - 1996 DA - 1996// TI - Among-site rate variation and its impact on phylogenetic analyses JO - Trends in Ecology & Evolution VL - 11 UR - https://doi.org/10.1016/0169-5347(96)10041-0 DO - 10.1016/0169-5347(96)10041-0 ID - Yang1996 ER - TY - JOUR AU - Gu, X. AU - Fu, Y. X. AU - Li, W. H. PY - 1995 DA - 1995// TI - Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites JO - Mol biol evol VL - 12 ID - Gu1995 ER - TY - JOUR AU - Guindon, S. AU - Gascuel, O. PY - 2003 DA - 2003// TI - A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood JO - Syst Biol VL - 52 UR - https://doi.org/10.1080/10635150390235520 DO - 10.1080/10635150390235520 ID - Guindon2003 ER - TY - JOUR AU - Stamatakis, A. 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 AU - Saitou, N. AU - Nei, M. PY - 1987 DA - 1987// TI - The neighbor-joining method: a new method for reconstructing phylogenetic trees JO - Molecular Biology and Evolution VL - 4 ID - Saitou1987 ER - TY - CHAP AU - Felsenstein, J. PY - 2002 DA - 2002// BT - Inferring Phylogenies PB - Sinauer Associates Inc CY - Sunderland ID - Felsenstein2002 ER - TY - CHAP AU - Zwickl, D. J. PY - 2006 DA - 2006// BT - Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion PB - The University of Texas CY - Austin, TX, USA. ID - Zwickl2006 ER - TY - JOUR AU - Kirkpatrick, S. AU - Gelatt, C. D. AU - Vecchi, M. P. PY - 1983 DA - 1983// TI - Optimization by Simulated Annealing JO - Science VL - 220 UR - https://doi.org/10.1126/science.220.4598.671 DO - 10.1126/science.220.4598.671 ID - Kirkpatrick1983 ER - TY - JOUR AU - Lundy, M. PY - 1985 DA - 1985// TI - Applications of the Annealing Algorithm to Combinatorial Problems in Statistics JO - Biometrika VL - 72 UR - https://doi.org/10.1093/biomet/72.1.191 DO - 10.1093/biomet/72.1.191 ID - Lundy1985 ER - TY - CHAP AU - Holland, J. PY - 1975 DA - 1975// BT - Adaptation in Natural and Artificial Systems PB - University of Michigan Press CY - Ann Arbor ID - Holland1975 ER - TY - JOUR AU - Maddison, D. R. AU - Swofford, D. L. AU - Maddison, W. P. PY - 1997 DA - 1997// TI - NEXUS: an extensible file format for systematic information JO - Syst Biol VL - 46 UR - https://doi.org/10.1093/sysbio/46.4.590 DO - 10.1093/sysbio/46.4.590 ID - Maddison1997 ER - TY - JOUR AU - Posada, D. AU - Crandall, K. A. PY - 2001 DA - 2001// TI - Selecting the best-fit model of nucleotide substitution JO - Syst Biol VL - 50 UR - https://doi.org/10.1080/106351501750435121 DO - 10.1080/106351501750435121 ID - Posada2001 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 -