TY - JOUR AU - Rodriguez-Ezpeleta, N. AU - Brinkmann, H. AU - Burger, G. AU - Roger, A. J. AU - Gray, M. W. AU - Philippe, H. AU - Lang, B. F. PY - 2007 DA - 2007// TI - Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans JO - Curr Biol VL - 17 UR - https://doi.org/10.1016/j.cub.2007.07.036 DO - 10.1016/j.cub.2007.07.036 ID - Rodriguez-Ezpeleta2007 ER - TY - JOUR AU - Qiu, Y. L. AU - Lee, J. AU - Bernasconi-Quadroni, F. AU - Soltis, D. E. AU - Soltis, P. S. AU - Zanis, M. AU - Zimmer, E. A. AU - Chen, Z. AU - Savolainen, V. AU - Chase, M. W. PY - 1999 DA - 1999// TI - The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes JO - Nature VL - 402 UR - https://doi.org/10.1038/46536 DO - 10.1038/46536 ID - Qiu1999 ER - TY - JOUR AU - Madsen, O. AU - Scally, M. AU - Douady, C. J. AU - Kao, D. J. AU - DeBry, R. W. AU - Adkins, R. AU - Amrine, H. M. AU - Stanhope, M. J. AU - de Jong, W. W. AU - Springer, M. S. PY - 2001 DA - 2001// TI - Parallel adaptive radiations in two major clades of placental mammals JO - Nature VL - 409 UR - https://doi.org/10.1038/35054544 DO - 10.1038/35054544 ID - Madsen2001 ER - TY - JOUR AU - Dunn, C. W. AU - Hejnol, A. AU - Matus, D. Q. AU - Pang, K. AU - Browne, W. E. AU - Smith, S. A. AU - Seaver, E. AU - Rouse, G. W. AU - Obst, M. AU - Edgecombe, G. D. PY - 2008 DA - 2008// TI - Broad phylogenomic sampling improves resolution of the animal tree of life JO - Nature VL - 452 UR - https://doi.org/10.1038/nature06614 DO - 10.1038/nature06614 ID - Dunn2008 ER - TY - JOUR AU - Philippe, H. AU - Derelle, R. AU - Lopez, P. AU - Pick, K. AU - Borchiellini, C. AU - Boury-Esnault, N. AU - Vacelet, J. AU - Renard, E. AU - Houliston, E. AU - Queinnec, E. PY - 2009 DA - 2009// TI - Phylogenomics revives traditional views on deep animal relationships JO - Curr Biol VL - 19 UR - https://doi.org/10.1016/j.cub.2009.02.052 DO - 10.1016/j.cub.2009.02.052 ID - Philippe2009 ER - TY - JOUR AU - Delsuc, F. AU - Brinkmann, H. AU - Philippe, H. PY - 2005 DA - 2005// TI - Phylogenomics and the reconstruction of the tree of life JO - Nat Rev Genet VL - 6 UR - https://doi.org/10.1038/nrg1603 DO - 10.1038/nrg1603 ID - Delsuc2005 ER - TY - JOUR AU - Rokas, A. AU - Kruger, D. AU - Carroll, S. B. PY - 2005 DA - 2005// TI - Animal evolution and the molecular signature of radiations compressed in time JO - Science VL - 310 UR - https://doi.org/10.1126/science.1116759 DO - 10.1126/science.1116759 ID - Rokas2005 ER - TY - JOUR AU - Rodriguez-Ezpeleta, N. AU - Brinkmann, H. AU - Roure, B. AU - Lartillot, N. AU - Lang, B. F. AU - Philippe, H. PY - 2007 DA - 2007// TI - Detecting and overcoming systematic errors in genome-scale phylogenies JO - Syst Biol VL - 56 UR - https://doi.org/10.1080/10635150701397643 DO - 10.1080/10635150701397643 ID - Rodriguez-Ezpeleta2007 ER - TY - JOUR AU - Whitfield, J. B. AU - Lockhart, P. J. PY - 2007 DA - 2007// TI - Deciphering ancient rapid radiations JO - Trends Ecol Evol VL - 22 UR - https://doi.org/10.1016/j.tree.2007.01.012 DO - 10.1016/j.tree.2007.01.012 ID - Whitfield2007 ER - TY - JOUR AU - Baurain, D. AU - Brinkmann, H. AU - Philippe, H. PY - 2007 DA - 2007// TI - Lack of resolution in the animal phylogeny: closely spaced cladogeneses or undetected systematic errors? JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msl137 DO - 10.1093/molbev/msl137 ID - Baurain2007 ER - TY - JOUR AU - Phillips, M. J. AU - Delsuc, F. AU - Penny, D. PY - 2004 DA - 2004// TI - Genome-scale phylogeny and the detection of systematic biases JO - Molecular Biology and Evolution VL - 21 UR - https://doi.org/10.1093/molbev/msh137 DO - 10.1093/molbev/msh137 ID - Phillips2004 ER - TY - JOUR AU - Jeffroy, O. AU - Brinkmann, H. AU - Delsuc, F. AU - Philippe, H. PY - 2006 DA - 2006// TI - Phylogenomics: the beginning of incongruence? JO - Trends Genet VL - 22 UR - https://doi.org/10.1016/j.tig.2006.02.003 DO - 10.1016/j.tig.2006.02.003 ID - Jeffroy2006 ER - TY - CHAP AU - Jukes, T. H. AU - Cantor, C. R. ED - Munro, H. N. PY - 1969 DA - 1969// TI - Evolution of protein molecules BT - Mammalian protein metabolism PB - Academic Press CY - New York UR - https://doi.org/10.1016/B978-1-4832-3211-9.50009-7 DO - 10.1016/B978-1-4832-3211-9.50009-7 ID - Jukes1969 ER - TY - CHAP AU - Dayhoff, M. O. AU - Eck, R. V. AU - Park, C. M. ED - Dayhoff, M. O. PY - 1972 DA - 1972// TI - A model of evolutionary change in proteins BT - Atlas of protein sequence and structure PB - National Biomedical Research Fundation CY - Washington, DC ID - Dayhoff1972 ER - TY - JOUR AU - Yang, Z. AU - Roberts, D. PY - 1995 DA - 1995// TI - On the use of nucleic acid sequences to infer early branchings in the tree of life JO - Mol Biol Evol VL - 12 ID - Yang1995 ER - TY - JOUR AU - Yang, Z. PY - 1993 DA - 1993// TI - Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites JO - Mol Biol Evol VL - 10 ID - Yang1993 ER - TY - JOUR AU - Goldman, N. AU - Thorne, J. L. AU - Jones, D. T. PY - 1998 DA - 1998// TI - Assessing the impact of secondary structure and solvent accessibility on protein evolution JO - Genetics VL - 149 ID - Goldman1998 ER - TY - JOUR AU - Thorne, J. L. AU - Goldman, N. AU - Jones, D. T. PY - 1996 DA - 1996// TI - Combining protein evolution and secondary structure JO - Mol Biol Evol VL - 13 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025627 DO - 10.1093/oxfordjournals.molbev.a025627 ID - Thorne1996 ER - TY - JOUR AU - Koshi, J. M. AU - Mindell, D. P. AU - Goldstein, R. A. PY - 1997 DA - 1997// TI - Beyond Mutation Matrices: Physical-Chemistry Based Evolutionary Models JO - Genome Inform Ser Workshop Genome Inform VL - 8 ID - Koshi1997 ER - TY - JOUR AU - Koshi, J. M. AU - Mindell, D. P. AU - Goldstein, R. A. PY - 1999 DA - 1999// TI - Using physical-chemistry-based substitution models in phylogenetic analyses of HIV-1 subtypes JO - Mol Biol Evol VL - 16 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026100 DO - 10.1093/oxfordjournals.molbev.a026100 ID - Koshi1999 ER - TY - JOUR AU - Bruno, W. J. PY - 1996 DA - 1996// TI - Modeling residue usage in aligned protein sequences via maximum likelihood JO - Molecular Biology and Evolution VL - 13 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025583 DO - 10.1093/oxfordjournals.molbev.a025583 ID - Bruno1996 ER - TY - CHAP AU - Dimmic, M. W. AU - Mindell, D. P. AU - Goldstein, R. A. PY - 2000 DA - 2000// TI - Modeling evolution at the protein level using an adjustable amino acid fitness model BT - Pac Symp Biocomput ID - Dimmic2000 ER - TY - JOUR AU - Pagel, M. AU - Meade, A. PY - 2004 DA - 2004// TI - A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data JO - Syst Biol VL - 53 UR - https://doi.org/10.1080/10635150490468675 DO - 10.1080/10635150490468675 ID - Pagel2004 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 - Molecular Biology and Evolution VL - 21 UR - https://doi.org/10.1093/molbev/msh112 DO - 10.1093/molbev/msh112 ID - Lartillot2004 ER - TY - JOUR AU - Wang, H. C. AU - Li, K. AU - Susko, E. AU - Roger, A. J. PY - 2008 DA - 2008// TI - A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny JO - BMC Evol Biol VL - 8 UR - https://doi.org/10.1186/1471-2148-8-331 DO - 10.1186/1471-2148-8-331 ID - Wang2008 ER - TY - JOUR AU - Ferguson, T. PY - 1973 DA - 1973// TI - A Bayesian analysis of some nonparametric problems JO - Ann Statistics VL - 1 UR - https://doi.org/10.1214/aos/1176342360 DO - 10.1214/aos/1176342360 ID - Ferguson1973 ER - TY - JOUR AU - Lartillot, N. AU - Philippe, H. PY - 2008 DA - 2008// TI - Improvement of molecular phylogenetic inference and the phylogeny of Bilateria JO - Philos Trans R Soc Lond B Biol Sci VL - 363 UR - https://doi.org/10.1098/rstb.2007.2236 DO - 10.1098/rstb.2007.2236 ID - Lartillot2008 ER - TY - JOUR AU - Sperling, E. A. AU - Peterson, K. J. AU - Pisani, D. PY - 2009 DA - 2009// TI - Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa JO - Mol Biol Evol VL - 26 UR - https://doi.org/10.1093/molbev/msp148 DO - 10.1093/molbev/msp148 ID - Sperling2009 ER - TY - JOUR AU - Rota-Stabelli, O. AU - Kayal, E. AU - Gleeson, D. AU - Daub, J. AU - Boore, J. L. AU - Telford, M. J. AU - Pisani, D. AU - Blaxter, M. AU - Lavrov, D. V. PY - 2010 DA - 2010// TI - Ecdysozoan mitogenomics: evidence for a common origin of the legged invertebrates, the Panarthropoda JO - Genome biology and evolution VL - 2 UR - https://doi.org/10.1093/gbe/evq030 DO - 10.1093/gbe/evq030 ID - Rota-Stabelli2010 ER - TY - JOUR AU - Lartillot, N. AU - Lepage, T. AU - Blanquart, S. PY - 2009 DA - 2009// TI - PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp368 DO - 10.1093/bioinformatics/btp368 ID - Lartillot2009 ER - TY - JOUR AU - Lartillot, N. AU - Brinkmann, H. AU - Philippe, H. PY - 2007 DA - 2007// TI - Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model JO - BMC Evol Biol VL - 7 UR - https://doi.org/10.1186/1471-2148-7-S1-S4 DO - 10.1186/1471-2148-7-S1-S4 ID - Lartillot2007 ER - TY - JOUR AU - Philippe, H. AU - Brinkmann, H. AU - Martinez, P. AU - Riutort, M. AU - Baguna, J. PY - 2007 DA - 2007// TI - Acoel flatworms are not platyhelminthes: evidence from phylogenomics JO - PLoS ONE VL - 2 UR - https://doi.org/10.1371/journal.pone.0000717 DO - 10.1371/journal.pone.0000717 ID - Philippe2007 ER - TY - JOUR AU - Delsuc, F. AU - Tsagkogeorga, G. AU - Lartillot, N. AU - Philippe, H. PY - 2008 DA - 2008// TI - Additional molecular support for the new chordate phylogeny JO - Genesis VL - 46 UR - https://doi.org/10.1002/dvg.20450 DO - 10.1002/dvg.20450 ID - Delsuc2008 ER - TY - JOUR AU - Bourlat, S. J. AU - Rota-Stabelli, O. AU - Lanfear, R. AU - Telford, M. J. PY - 2009 DA - 2009// TI - The mitochondrial genome structure of Xenoturbella bocki (phylum Xenoturbellida) is ancestral within the deuterostomes JO - BMC Evol Biol VL - 9 UR - https://doi.org/10.1186/1471-2148-9-107 DO - 10.1186/1471-2148-9-107 ID - Bourlat2009 ER - TY - JOUR AU - Fitch, W. M. PY - 1971 DA - 1971// TI - The nonidentity of invariable positions in the cytochromes c of different species JO - Biochem Genet VL - 5 UR - https://doi.org/10.1007/BF00485794 DO - 10.1007/BF00485794 ID - Fitch1971 ER - TY - JOUR AU - Penny, D. AU - McComish, B. J. AU - Charleston, M. A. AU - Hendy, M. D. PY - 2001 DA - 2001// TI - Mathematical elegance with biochemical realism: the covarion model of molecular evolution JO - J Mol Evol VL - 53 UR - https://doi.org/10.1007/s002390010258 DO - 10.1007/s002390010258 ID - Penny2001 ER - TY - JOUR AU - Philippe, H. AU - Lopez, P. PY - 2001 DA - 2001// TI - On the conservation of protein sequences in evolution JO - Trends in Biochemical Sciences VL - 26 UR - https://doi.org/10.1016/S0968-0004(01)01877-1 DO - 10.1016/S0968-0004(01)01877-1 ID - Philippe2001 ER - TY - JOUR AU - Lockhart, P. J. AU - Huson, D. AU - Maier, U. AU - Fraunholz, M. J. AU - Van De Peer, Y. AU - Barbrook, A. C. AU - Howe, C. J. AU - Steel, M. A. PY - 2000 DA - 2000// TI - How molecules evolve in Eubacteria JO - Mol Biol Evol VL - 17 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026363 DO - 10.1093/oxfordjournals.molbev.a026363 ID - Lockhart2000 ER - TY - JOUR AU - Lopez, P. AU - Casane, D. AU - Philippe, H. PY - 2002 DA - 2002// TI - Heterotachy, an important process of protein evolution JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003973 DO - 10.1093/oxfordjournals.molbev.a003973 ID - Lopez2002 ER - TY - JOUR AU - Baele, G. AU - Raes, J. AU - Van de Peer, Y. AU - Vansteelandt, S. PY - 2006 DA - 2006// TI - An improved statistical method for detecting heterotachy in nucleotide sequences JO - Mol Biol Evol VL - 23 UR - https://doi.org/10.1093/molbev/msl006 DO - 10.1093/molbev/msl006 ID - Baele2006 ER - TY - JOUR AU - Fitch, W. M. AU - Markowitz, E. PY - 1970 DA - 1970// TI - An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution JO - Biochem Genet VL - 4 UR - https://doi.org/10.1007/BF00486096 DO - 10.1007/BF00486096 ID - Fitch1970 ER - TY - JOUR AU - Galtier, N. PY - 2001 DA - 2001// TI - Maximum-likelihood phylogenetic analysis under a covarion-like model JO - Mol Biol Evol VL - 18 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003868 DO - 10.1093/oxfordjournals.molbev.a003868 ID - Galtier2001 ER - TY - JOUR AU - Huelsenbeck, J. P. PY - 2002 DA - 2002// TI - Testing a covariotide model of DNA substitution JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a004128 DO - 10.1093/oxfordjournals.molbev.a004128 ID - Huelsenbeck2002 ER - TY - JOUR AU - Wang, H. C. AU - Spencer, M. AU - Susko, E. AU - Roger, A. J. PY - 2007 DA - 2007// TI - Testing for covarion-like evolution in protein sequences JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msl155 DO - 10.1093/molbev/msl155 ID - Wang2007 ER - TY - JOUR AU - Kolaczkowski, B. AU - Thornton, J. W. PY - 2004 DA - 2004// TI - Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous JO - Nature VL - 431 UR - https://doi.org/10.1038/nature02917 DO - 10.1038/nature02917 ID - Kolaczkowski2004 ER - TY - JOUR AU - Dorman, K. S. PY - 2007 DA - 2007// TI - Identifying dramatic selection shifts in phylogenetic trees JO - BMC Evol Biol VL - 7 UR - https://doi.org/10.1186/1471-2148-7-S1-S10 DO - 10.1186/1471-2148-7-S1-S10 ID - Dorman2007 ER - TY - JOUR AU - Rodrigue, N. AU - Philippe, H. AU - Lartillot, N. PY - 2010 DA - 2010// TI - Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles JO - Proc Natl Acad Sci USA VL - 107 UR - https://doi.org/10.1073/pnas.0910915107 DO - 10.1073/pnas.0910915107 ID - Rodrigue2010 ER - TY - JOUR AU - Yoder, A. D. AU - Yang, Z. PY - 2000 DA - 2000// TI - Estimation of primate speciation dates using local molecular clocks JO - Mol Biol Evol VL - 17 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026389 DO - 10.1093/oxfordjournals.molbev.a026389 ID - Yoder2000 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 - Mol Biol Evol VL - 15 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025892 DO - 10.1093/oxfordjournals.molbev.a025892 ID - Thorne1998 ER - TY - JOUR AU - Foster, P. G. AU - Hickey, D. A. PY - 1999 DA - 1999// TI - Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions JO - J Mol Evol VL - 48 UR - https://doi.org/10.1007/PL00006471 DO - 10.1007/PL00006471 ID - Foster1999 ER - TY - JOUR AU - Haen, K. M. AU - Lang, B. F. AU - Pomponi, S. A. AU - Lavrov, D. V. PY - 2007 DA - 2007// TI - Glass sponges and bilaterian animals share derived mitochondrial genomic features: a common ancestry or parallel evolution? JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msm070 DO - 10.1093/molbev/msm070 ID - Haen2007 ER - TY - JOUR AU - Wang, X. AU - Lavrov, D. V. PY - 2007 DA - 2007// TI - Mitochondrial genome of the homoscleromorph Oscarella carmela (Porifera, Demospongiae) reveals unexpected complexity in the common ancestor of sponges and other animals JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msl167 DO - 10.1093/molbev/msl167 ID - Wang2007 ER - TY - JOUR AU - Pisani, D. PY - 2004 DA - 2004// TI - Identifying and removing fast-evolving sites using compatibility analysis: An example from the arthropoda JO - Systematic Biology VL - 53 UR - https://doi.org/10.1080/10635150490888877 DO - 10.1080/10635150490888877 ID - Pisani2004 ER - TY - JOUR AU - Brinkmann, H. AU - Philippe, H. PY - 1999 DA - 1999// TI - Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies JO - Molecular Biology and Evolution VL - 16 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026166 DO - 10.1093/oxfordjournals.molbev.a026166 ID - Brinkmann1999 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 - JOUR AU - Dayhoff, M. O. AU - Barker, W. C. AU - McLaughlin, P. J. PY - 1974 DA - 1974// TI - Inferences from protein and nucleic acid sequences: early molecular evolution, divergence of kingdoms and rates of change JO - Orig Life VL - 5 UR - https://doi.org/10.1007/BF01207633 DO - 10.1007/BF01207633 ID - Dayhoff1974 ER - TY - JOUR AU - Yang, Z. PY - 1996 DA - 1996// TI - Among-site rate variation and its impact on phylogenetic analyses JO - Trends Ecol Evol 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 - Lockhart, P. AU - Steel, M. AU - Hendy, M. AU - Penny, D. PY - 1994 DA - 1994// TI - Recovering evolutionary trees under a more realistic model of sequence evolution JO - Molecular Biology and Evolution VL - 11 ID - Lockhart1994 ER - TY - JOUR AU - Schwartz, R. S. AU - Mueller, R. L. PY - 2010 DA - 2010// TI - Limited effects of among-lineage rate variation on the phylogenetic performance of molecular markers JO - Mol Phylogenet Evol VL - 54 UR - https://doi.org/10.1016/j.ympev.2009.12.025 DO - 10.1016/j.ympev.2009.12.025 ID - Schwartz2010 ER - TY - JOUR AU - Tuffley, C. AU - Steel, M. PY - 1998 DA - 1998// TI - Modeling the covarion hypothesis of nucleotide substitution JO - Math Biosci VL - 147 UR - https://doi.org/10.1016/S0025-5564(97)00081-3 DO - 10.1016/S0025-5564(97)00081-3 ID - Tuffley1998 ER - TY - JOUR AU - Huelsenbeck, J. P. AU - Larget, B. AU - Swofford, D. PY - 2000 DA - 2000// TI - A compound poisson process for relaxing the molecular clock JO - Genetics VL - 154 ID - Huelsenbeck2000 ER - TY - JOUR AU - Thompson, J. D. AU - Higgins, D. G. AU - Gibson, T. J. PY - 1994 DA - 1994// TI - CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice JO - Nucleic Acids Res VL - 22 UR - https://doi.org/10.1093/nar/22.22.4673 DO - 10.1093/nar/22.22.4673 ID - Thompson1994 ER - TY - JOUR AU - Philippe, H. PY - 1993 DA - 1993// TI - MUST, a computer package of Management Utilities for Sequences and Trees JO - Nucleic Acids Res VL - 21 UR - https://doi.org/10.1093/nar/21.22.5264 DO - 10.1093/nar/21.22.5264 ID - Philippe1993 ER - TY - JOUR AU - Roure, B. AU - Rodriguez-Ezpeleta, N. AU - Philippe, H. PY - 2007 DA - 2007// TI - SCaFoS: a tool for Selection, Concatenation and Fusion of Sequences for phylogenomics JO - BMC Evol Biol VL - 7 UR - https://doi.org/10.1186/1471-2148-7-S1-S2 DO - 10.1186/1471-2148-7-S1-S2 ID - Roure2007 ER - TY - JOUR AU - Castresana, J. PY - 2000 DA - 2000// TI - Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis JO - Mol Biol Evol VL - 17 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026334 DO - 10.1093/oxfordjournals.molbev.a026334 ID - Castresana2000 ER - TY - JOUR AU - Whelan, S. AU - Goldman, N. PY - 2001 DA - 2001// TI - A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach JO - Mol Biol Evol VL - 18 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003851 DO - 10.1093/oxfordjournals.molbev.a003851 ID - Whelan2001 ER - TY - JOUR AU - Adachi, J. AU - Hasegawa, M. PY - 1996 DA - 1996// TI - Model of amino acid substitution in proteins encoded by mitochondrial DNA JO - Journal of Molecular Evolution VL - 42 UR - https://doi.org/10.1007/BF02498640 DO - 10.1007/BF02498640 ID - Adachi1996 ER - TY - JOUR AU - Jobb, G. AU - von Haeseler, A. AU - Strimmer, K. PY - 2004 DA - 2004// TI - TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics JO - BMC Evol Biol VL - 4 UR - https://doi.org/10.1186/1471-2148-4-18 DO - 10.1186/1471-2148-4-18 ID - Jobb2004 ER - TY - CHAP AU - Felsenstein, J. PY - 2001 DA - 2001// BT - PHYLIP (Phylogene Inference Package) PB - Distributed by the author, Department of Genetics, University of Washington CY - Seattle ID - Felsenstein2001 ER - TY - JOUR AU - Le, S. Q. AU - Gascuel, O. AU - Lartillot, N. PY - 2008 DA - 2008// TI - Empirical profile mixture models for phylogenetic reconstruction JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn445 DO - 10.1093/bioinformatics/btn445 ID - Le2008 ER - TY - JOUR AU - Inagaki, Y. AU - Susko, E. AU - Fast, N. M. AU - Roger, A. J. PY - 2004 DA - 2004// TI - Covarion shifts cause a long-branch attraction artifact that unites Microsporidia and Archaebacteria in EF-1α phylogenies JO - Mol Biol Evol VL - 21 UR - https://doi.org/10.1093/molbev/msh130 DO - 10.1093/molbev/msh130 ID - Inagaki2004 ER - TY - JOUR AU - Philippe, H. AU - Germot, A. PY - 2000 DA - 2000// TI - Phylogeny of eukaryotes based on ribosomal RNA: long-branch attraction and models of sequence evolution JO - Mol Biol Evol VL - 17 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026362 DO - 10.1093/oxfordjournals.molbev.a026362 ID - Philippe2000 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 - Lopez, P. AU - Forterre, P. AU - Philippe, H. PY - 1999 DA - 1999// TI - The root of the tree of life in the light of the covarion model JO - Journal of Molecular Evolution VL - 49 UR - https://doi.org/10.1007/PL00006572 DO - 10.1007/PL00006572 ID - Lopez1999 ER - TY - JOUR AU - Kyte, J. AU - Doolittle, R. F. PY - 1982 DA - 1982// TI - A simple method for displaying the hydropathic character of a protein JO - J Mol Biol VL - 157 UR - https://doi.org/10.1016/0022-2836(82)90515-0 DO - 10.1016/0022-2836(82)90515-0 ID - Kyte1982 ER -