TY - CHAP AU - Lecointre, G. AU - Le Guyader, H. PY - 2001 DA - 2001// BT - Classification phylogénétique du vivant PB - Paris CY - Belin ID - Lecointre2001 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 - CHAP AU - Li, W. H. ED - Sinauer, A. PY - 1997 DA - 1997// BT - Molecular Evolution ID - Li1997 ER - TY - JOUR AU - Higgins, D. G. AU - Thompson, J. D. AU - Gibson, T. J. PY - 1996 DA - 1996// TI - Using CLUSTAL for multiple sequence alignments JO - Methods Enzymol VL - 266 UR - https://doi.org/10.1016/S0076-6879(96)66024-8 DO - 10.1016/S0076-6879(96)66024-8 ID - Higgins1996 ER - TY - JOUR AU - Brocchieri, L. PY - 2001 DA - 2001// TI - Phylogenetic inferences from molecular sequences: review and critique JO - Theor Popul Biol VL - 59 UR - https://doi.org/10.1006/tpbi.2000.1485 DO - 10.1006/tpbi.2000.1485 ID - Brocchieri2001 ER - TY - JOUR AU - Russo, C. A. M. AU - Takezaki, N. AU - Nei, M. PY - 1996 DA - 1996// TI - Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny JO - Mol Biol Evol VL - 13 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025613 DO - 10.1093/oxfordjournals.molbev.a025613 ID - Russo1996 ER - TY - JOUR AU - Billoud, B. AU - Guerrucci, M. A. AU - Masselot, M. AU - Deutsch, J. S. PY - 2000 DA - 2000// TI - Cirripede phylogeny using a novel approach: molecular morphometrics JO - Mol Biol Evol VL - 17 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026244 DO - 10.1093/oxfordjournals.molbev.a026244 ID - Billoud2000 ER - TY - JOUR AU - Wolf, Y. I. AU - Rogozin, I. B. AU - Grishin, N. V. AU - Tatusov, R. L. AU - Koonin, E. V. PY - 2001 DA - 2001// TI - Genome trees constructed using five different approaches suggest new major bacterial clades JO - BMC Evol Biol VL - 1 UR - https://doi.org/10.1186/1471-2148-1-8 DO - 10.1186/1471-2148-1-8 ID - Wolf2001 ER - TY - JOUR AU - Korbel, J. O. AU - Snel, B. AU - Huynen, M. A. AU - Bork, P. PY - 2002 DA - 2002// TI - SHOT: a web server for the construction of genome phylogenies JO - Trends Genet VL - 18 UR - https://doi.org/10.1016/S0168-9525(01)02597-5 DO - 10.1016/S0168-9525(01)02597-5 ID - Korbel2002 ER - TY - JOUR AU - Tekaia, F. AU - Lazcano, A. AU - Dujon, B. PY - 1999 DA - 1999// TI - The genomic tree as revealed from whole proteome comparisons JO - Genome Res VL - 9 ID - Tekaia1999 ER - TY - JOUR AU - Daubin, V. AU - Gouy, M. AU - Perrière, G. PY - 2002 DA - 2002// TI - A phylogenetic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. JO - Genome Research VL - 12 UR - https://doi.org/10.1101/gr.187002 DO - 10.1101/gr.187002 ID - Daubin2002 ER - TY - JOUR AU - Gupta, R. S. PY - 1998 DA - 1998// TI - Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among Archaebacteria, Eubacteria and Eukaryotes. JO - Microbiol Mol Biol Rev VL - 62 ID - Gupta1998 ER - TY - JOUR AU - Rivera, M. C. AU - Lake, J. A. PY - 1992 DA - 1992// TI - Evidence that eukaryotes and eocyte prokaryotes are immediate relatives JO - Science VL - 257 UR - https://doi.org/10.1126/science.1621096 DO - 10.1126/science.1621096 ID - Rivera1992 ER - TY - JOUR AU - Karlin, S. AU - Burge, C. PY - 1995 DA - 1995// TI - Dinucleotide relative abundance extremes: a genomic signature JO - Trends In Genetics VL - 11 UR - https://doi.org/10.1016/S0168-9525(00)89076-9 DO - 10.1016/S0168-9525(00)89076-9 ID - Karlin1995 ER - TY - JOUR AU - Pride, D. T. AU - Meinersmann, R. J. AU - Wassenaar, T. M. AU - Blaser, M. J. PY - 2003 DA - 2003// TI - Evolutionary implications of microbial genome tetranucleotide frequency biases JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.335003 DO - 10.1101/gr.335003 ID - Pride2003 ER - TY - JOUR AU - Yu, Z. G. AU - Jiang, P. PY - 2001 DA - 2001// TI - Distance, correlation and mutual information among portraits of organisms based on complete genomes JO - Phys Lett A VL - 286 UR - https://doi.org/10.1016/S0375-9601(01)00336-X DO - 10.1016/S0375-9601(01)00336-X ID - Yu2001 ER - TY - JOUR AU - Qi, J. AU - Wang, B. AU - Hao, B. I. PY - 2004 DA - 2004// TI - Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach JO - J Mol Evol VL - 58 UR - https://doi.org/10.1007/s00239-003-2493-7 DO - 10.1007/s00239-003-2493-7 ID - Qi2004 ER - TY - JOUR AU - Stuart, G. W. AU - Moffett, K. AU - Leader, J. J. PY - 2002 DA - 2002// TI - A comprehensive vertebrate phylogeny using vector representations of protein sequences from whole genomes JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a004111 DO - 10.1093/oxfordjournals.molbev.a004111 ID - Stuart2002 ER - TY - JOUR AU - Deschavanne, P. J. AU - Giron, A. AU - Vilain, J. AU - Fagot, G. AU - Fertil, B. PY - 1999 DA - 1999// TI - Genomic signature: characterization and classification of species assessed by Chaos Game Representation of sequences JO - Molecular Biology and Evolution VL - 16 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026048 DO - 10.1093/oxfordjournals.molbev.a026048 ID - Deschavanne1999 ER - TY - CHAP AU - Deschavanne, P. AU - Giron, A. AU - Vilain, J. AU - Dufraigne, C. AU - Fertil, B. PY - 2000 DA - 2000// TI - Genomic signature is preserved in short DNA fragments BT - BIBE2000 IEEE international Symposium on bio-informatics & biomedical engineering, Washington USA, 8-10 november 2000 ID - Deschavanne2000 ER - TY - CHAP AU - Chapus, C. AU - Fertil, B. AU - Edwars, S. AU - Giron, A. AU - Deschavanne, P. ED - Spang, R. ED - Béziat, P. ED - Vingron, M. PY - 2003 DA - 2003// BT - Classification of species based on DNA style: ; Berlin, Germany. ID - Chapus2003 ER - TY - JOUR AU - Karlin, S. PY - 1999 DA - 1999// TI - Bacterial DNA strand compositional asymmetry JO - Trends Microbiol VL - 7 UR - https://doi.org/10.1016/S0966-842X(99)01541-3 DO - 10.1016/S0966-842X(99)01541-3 ID - Karlin1999 ER - TY - JOUR AU - Karlin, S. AU - Mràzek, J. AU - Campbell, A. M. PY - 1997 DA - 1997// TI - Compositional biases of bacterial genomes and evolutionary implications JO - J Bact VL - 179 ID - Karlin1997 ER - TY - JOUR AU - Edwards, S. V. AU - Fertil, B. AU - Giron, A. AU - Deschavanne, P. J. PY - 2002 DA - 2002// TI - A genomic schism in birds revealed by phylogenetic analysis of DNA strings JO - Syst Biol VL - 51 UR - https://doi.org/10.1080/10635150290102285 DO - 10.1080/10635150290102285 ID - Edwards2002 ER - TY - JOUR AU - Wang, Y. AU - Hill, K. AU - Singh, S. AU - Kari, L. PY - 2005 DA - 2005// TI - The spectrum of genomic signatures: from dinucleotides to chaos game representation JO - Gene VL - 346 UR - https://doi.org/10.1016/j.gene.2004.10.021 DO - 10.1016/j.gene.2004.10.021 ID - Wang2005 ER - TY - STD TI - Guénoche A, Garreta H: 2000, Springer, 2066: 45-56. Can We Have Confidence in a Tree Representation?: 2001; Montpelier, France., Gascuel O and Sagot MF, Lecture Notes in Computer Science, Goos G, Hartmanis J, van Leeuwen J, ID - ref26 ER - TY - JOUR AU - Daubin, V. AU - Gouy, M. AU - Perriere, G. PY - 2002 DA - 2002// TI - A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.187002 DO - 10.1101/gr.187002 ID - Daubin2002 ER - TY - JOUR AU - Lerat, E. AU - Daubin, V. AU - Moran, N. A. PY - 2003 DA - 2003// TI - From gene trees to organismal phylogeny in prokaryotes: the case of the g-proteobacteria JO - PLOS Biology VL - 1 UR - https://doi.org/10.1371/journal.pbio.0000019 DO - 10.1371/journal.pbio.0000019 ID - Lerat2003 ER - TY - CHAP AU - Buneman, P. ED - Hobson, F. R. ED - Kendall, D. G. ED - Tautu, P. PY - 1971 DA - 1971// BT - Mathematics in the Archeological and Historial Sciences PB - Edinburgh CY - University Press ID - Buneman1971 ER - TY - JOUR AU - Robinson, D. F. AU - Foulds, L. R. PY - 1981 DA - 1981// TI - Comparaison of phylogenetic trees JO - Math Biosci VL - 53 UR - https://doi.org/10.1016/0025-5564(81)90043-2 DO - 10.1016/0025-5564(81)90043-2 ID - Robinson1981 ER - TY - JOUR AU - Kuhner, M. K. AU - Felsenstein, J. PY - 1994 DA - 1994// TI - A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates JO - Mol Biol Evol VL - 11 ID - Kuhner1994 ER - TY - JOUR AU - Penny, D. AU - Hendy, M. D. PY - 1985 DA - 1985// TI - The use of tree comparaison metrics JO - Systematic Zoology VL - 34 UR - https://doi.org/10.2307/2413347 DO - 10.2307/2413347 ID - Penny1985 ER - TY - JOUR AU - Kumar, S. PY - 1996 DA - 1996// TI - A stepwise algorithm for finding minimum evolution trees JO - Mol Biol Evol VL - 13 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025618 DO - 10.1093/oxfordjournals.molbev.a025618 ID - Kumar1996 ER - TY - JOUR AU - Ranwez, V. AU - Gascuel, O. PY - 2001 DA - 2001// TI - Quartet-based phylogenetic inference: improvements and limits JO - Mol Biol Evol VL - 18 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003881 DO - 10.1093/oxfordjournals.molbev.a003881 ID - Ranwez2001 ER - TY - STD TI - Gascuel O: http://www.lirmm.fr/~w3ifa/MAAS/US-MAAS.html. ID - ref35 ER - TY - JOUR AU - Rambaut, A. AU - Grassly, N. C. PY - 1997 DA - 1997// TI - Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees JO - Comput Appl Biosci VL - 13 ID - Rambaut1997 ER - TY - CHAP AU - Gascuel, O. ED - Baxevanis, A. ED - Davison, D. ED - Page, R. ED - Stein, L. ED - Stormo, G. ED - Petsko, G. ED - Wiley and Sons PY - 2004 DA - 2004// TI - Getting a Tree Fast: Neighbor Joining and Distance Based Methods BT - Current Protocols in Bioinformatics ID - Gascuel2004 ER - TY - JOUR AU - Greenhalgh, P. AU - Steiner, L. A. PY - 1995 DA - 1995// TI - Recombination activating gene 1 (Rag1) in zebrafish and shark JO - Immunogenetics VL - 41 UR - https://doi.org/10.1007/BF00188438 DO - 10.1007/BF00188438 ID - Greenhalgh1995 ER - TY - CHAP AU - Sibley, C. G. AU - Ahlquist, J. A. PY - 1990 DA - 1990// BT - Phylogeny and classification of birds: a study in molecular evolution PB - New Haven CY - Yale University Press ID - Sibley1990 ER - TY - JOUR AU - Feil, E. J. AU - Holmes, E. C. AU - Bessen, D. E. AU - Chan, M. S. AU - Day, N. P. AU - Enright, M. C. AU - Goldstein, R. AU - Hood, D. W. AU - Kalia, A. AU - Moore, C. E. AU - Zhou, J. AU - Spratt, B. G. PY - 2001 DA - 2001// TI - Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences JO - Proc Natl Acad Sci U S A VL - 98 UR - https://doi.org/10.1073/pnas.98.1.182 DO - 10.1073/pnas.98.1.182 ID - Feil2001 ER - TY - JOUR AU - Soltis, P. S. AU - Soltis, D. E. AU - Wolf, P. G. AU - Nickrent, D. L. AU - Chaw, S. M. AU - Chapman, R. L. PY - 1999 DA - 1999// TI - The phylogeny of land plants inferred from 18S rDNA sequences: pushing the limits of rDNA signal? JO - Mol Biol Evol VL - 16 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026089 DO - 10.1093/oxfordjournals.molbev.a026089 ID - Soltis1999 ER - TY - JOUR AU - Chaw, S. M. AU - Parkinson, C. L. AU - Cheng, Y. AU - Vincent, T. M. AU - Palmer, J. D. PY - 2000 DA - 2000// TI - Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers JO - Proc Natl Acad Sci U S A VL - 97 UR - https://doi.org/10.1073/pnas.97.8.4086 DO - 10.1073/pnas.97.8.4086 ID - Chaw2000 ER - TY - JOUR AU - Crane, P. R. PY - 1985 DA - 1985// TI - Phylogenetic analysis of seed plants and the origin of the angiosperms JO - Ann Mo Bot Gard VL - 72 UR - https://doi.org/10.2307/2399221 DO - 10.2307/2399221 ID - Crane1985 ER - TY - JOUR AU - Doyle, J. A. PY - 1996 DA - 1996// TI - Seed plant phylogeny and the relationshipsof Gnetales JO - Int J Plant Sci VL - 157 UR - https://doi.org/10.1086/297401 DO - 10.1086/297401 ID - Doyle1996 ER - TY - JOUR AU - Doyle, J. A. PY - 1998 DA - 1998// TI - Molecules, morphology, fossils, and the relationship of angiosperms and Gnetales JO - Mol Phylogenet Evol VL - 9 UR - https://doi.org/10.1006/mpev.1998.0506 DO - 10.1006/mpev.1998.0506 ID - Doyle1998 ER - TY - JOUR AU - Doyle, J. A. AU - Donoghue, M. J. PY - 1986 DA - 1986// TI - Seed plant phylogeny and the origin of the angiosperms: an experimental cladistic approach JO - Bot Rev VL - 52 UR - https://doi.org/10.1007/BF02861082 DO - 10.1007/BF02861082 ID - Doyle1986 ER - TY - JOUR AU - Doyle, J. A. AU - Donoghue, M. J. AU - Zimmer, E. A. PY - 1994 DA - 1994// TI - Integration of morphological and ribosomal RNA data on the origin of the angiosperms JO - Ann Mo Bot Gard VL - 81 UR - https://doi.org/10.2307/2399899 DO - 10.2307/2399899 ID - Doyle1994 ER - TY - JOUR AU - Doyle, J. A. PY - 1998 DA - 1998// TI - Phylogeny of vascular plants JO - Annu Rev Ecol Syst Biol VL - 29 ID - Doyle1998 ER - TY - JOUR AU - Källersjö, M. AU - Farris, J. S. AU - Chase, W. AU - Bremer, B. AU - Fay, M. F. AU - Humpries, C. J. AU - Petersen, G. AU - Seberg, O. AU - Bremer, K. PY - 1998 DA - 1998// TI - Simultaneous parsimony jackknife analysis of 2538 rbcl DNA sequences reveals upport for major clades of green plants, land plants, seed plants and flowering plants. JO - Plant Syst Evol VL - 213 UR - https://doi.org/10.1007/BF00985205 DO - 10.1007/BF00985205 ID - Källersjö1998 ER - TY - JOUR AU - Kenrick, P. AU - Crane, P. R. PY - 1997 DA - 1997// TI - The origin and early evolution of plants on land. JO - nature VL - 389 UR - https://doi.org/10.1038/37918 DO - 10.1038/37918 ID - Kenrick1997 ER - TY - JOUR AU - Manhart, J. R. PY - 1994 DA - 1994// TI - Phylogenetic analysis of green plant rbcL sequences JO - Mol Phylogenet Evol VL - 3 UR - https://doi.org/10.1006/mpev.1994.1014 DO - 10.1006/mpev.1994.1014 ID - Manhart1994 ER - TY - JOUR AU - Manhart, J. R. PY - 1995 DA - 1995// TI - Chloroplast 16S rDNA sequences and phylogeneic relationships of ferns and fern allies JO - Am Fern J VL - 85 UR - https://doi.org/10.2307/1547808 DO - 10.2307/1547808 ID - Manhart1995 ER - TY - JOUR AU - Rokas, A. AU - Williams, B. L. AU - King, N. AU - Carroll, S. B. PY - 2003 DA - 2003// TI - Genome-scale approaches to resolving incongruence in molecular phylogenies JO - Nature VL - 425 UR - https://doi.org/10.1038/nature02053 DO - 10.1038/nature02053 ID - Rokas2003 ER - TY - JOUR AU - Gray, M. W. AU - Burger, G. AU - Lang, B. F. PY - 1999 DA - 1999// TI - Mitochondrial evolution JO - Science VL - 283 UR - https://doi.org/10.1126/science.283.5407.1476 DO - 10.1126/science.283.5407.1476 ID - Gray1999 ER - TY - JOUR AU - Dufraigne, C. AU - Fertil, B. AU - Lespinats, S. AU - Giron, A. AU - Deschavanne, P. PY - 2005 DA - 2005// TI - Detection and characterization of horizontal transfers in prokaryotes using genomic signature JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gni004 DO - 10.1093/nar/gni004 ID - Dufraigne2005 ER - TY - JOUR AU - Garcia-Vallve, S. AU - Guzman, E. AU - Montero, M. A. AU - Romeu, A. PY - 2003 DA - 2003// TI - HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes JO - Nucleic Acids Research VL - 31 UR - https://doi.org/10.1093/nar/gkg004 DO - 10.1093/nar/gkg004 ID - Garcia-Vallve2003 ER - TY - JOUR AU - Nakamura, Y. AU - Itoh, T. AU - Matsuda, H. AU - Gojobori, T. PY - 2004 DA - 2004// TI - Biased biological functions of horizontally transferred genes in prokaryotic genomes JO - Nature Genetics VL - 36 UR - https://doi.org/10.1038/ng1381 DO - 10.1038/ng1381 ID - Nakamura2004 ER - TY - JOUR AU - Lanyon, S. M. PY - 1985 DA - 1985// TI - Detecting internal inconsistencies in distance data JO - Systematic Zoology VL - 34 UR - https://doi.org/10.2307/2413204 DO - 10.2307/2413204 ID - Lanyon1985 ER - TY - JOUR AU - Felsenstein, J. PY - 1978 DA - 1978// TI - Cases in wich parsimony or compability methods will be positively misleading. JO - Systematic Zoology VL - 27 UR - https://doi.org/10.2307/2412923 DO - 10.2307/2412923 ID - Felsenstein1978 ER - TY - JOUR AU - Moran, N. A. AU - Mira, A. PY - 2001 DA - 2001// TI - The process of genome shrinkage in the obligate symbiont Buchnera aphidicola JO - Genome Biol VL - 2 UR - https://doi.org/10.1186/gb-2001-2-12-research0054 DO - 10.1186/gb-2001-2-12-research0054 ID - Moran2001 ER - TY - JOUR AU - Itoh, T. AU - Martin, W. AU - Nei, M. PY - 2002 DA - 2002// TI - Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts JO - Proc Natl Acad Sci U S A VL - 99 UR - https://doi.org/10.1073/pnas.192449699 DO - 10.1073/pnas.192449699 ID - Itoh2002 ER - TY - JOUR AU - Yu, Z. G. AU - Anh, V. AU - Lau, K. S. PY - 2001 DA - 2001// TI - Measure representation and multifractal analysis of complete genomes JO - Phys Rev E VL - 64 ID - Yu2001 ER - TY - JOUR AU - Jeffrey, H. J. PY - 1990 DA - 1990// TI - Chaos game representation of gene structure JO - Nucleic Acids Research VL - 18 UR - https://doi.org/10.1093/nar/18.8.2163 DO - 10.1093/nar/18.8.2163 ID - Jeffrey1990 ER - TY - JOUR AU - Krause, A. AU - Stoye, J. AU - Vingron, M. PY - 2000 DA - 2000// TI - The SYSTERS protein sequence cluster set JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.270 DO - 10.1093/nar/28.1.270 ID - Krause2000 ER - TY - STD TI - GIB: http://gib.genes.nig.ac.jp/. ID - ref65 ER - TY - CHAP AU - Felsenstein, J. PY - 2004 DA - 2004// BT - PHYLIP (Phylogeny Inference Package) 3.6 ID - Felsenstein2004 ER - TY - JOUR AU - Felsenstein, J. PY - 1985 DA - 1985// TI - Confidence limits on phylogenies : an approach using the bootstrap JO - Evolution VL - 4 UR - https://doi.org/10.2307/2408678 DO - 10.2307/2408678 ID - Felsenstein1985 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 - Mol Biol Evol VL - 4 ID - Saitou1987 ER - TY - JOUR AU - Fitch, W. M. PY - 1977 DA - 1977// TI - On the problem of discovery the most parsimonious tree JO - Am Nat VL - 111 UR - https://doi.org/10.1086/283157 DO - 10.1086/283157 ID - Fitch1977 ER - TY - CHAP AU - Swofford, D. L. PY - 2003 DA - 2003// BT - PAUP*, Phylogenetic Analysis Using Parsimony (*and Other Methods) PB - Sinauer Associates CY - Sunderland, Massachusetts ID - Swofford2003 ER -