TY - JOUR AU - Needleman, S. AU - Wunsch, C. PY - 1970 DA - 1970// TI - A general method applicable to the search for similarities in the amino acid sequence of two proteins JO - J Mol Biol VL - 48 UR - https://doi.org/10.1016/0022-2836(70)90057-4 DO - 10.1016/0022-2836(70)90057-4 ID - Needleman1970 ER - TY - JOUR AU - Blaisdell, B. PY - 1986 DA - 1986// TI - A measure of the similarity of sets of sequences not requiring sequence alignment JO - PNAS VL - 83 UR - https://doi.org/10.1073/pnas.83.14.5155 DO - 10.1073/pnas.83.14.5155 ID - Blaisdell1986 ER - TY - JOUR AU - Blaisdell, B. PY - 1989 DA - 1989// TI - Average values of a dissimilarity measure not requiring sequence alignment are twice the average of conventional mismatch counts requiring sequence alignment for a computer-generated model system JO - J Mol Evol VL - 29 UR - https://doi.org/10.1007/BF02602925 DO - 10.1007/BF02602925 ID - Blaisdell1989 ER - TY - JOUR AU - Sims, G. AU - Jun, S. AU - Wu, G. AU - Kim, S. PY - 2009 DA - 2009// TI - Alignment-free genome comparison with feature frequency profiles(FFP) and optimal resolutions JO - PNAS VL - 106 UR - https://doi.org/10.1073/pnas.0813249106 DO - 10.1073/pnas.0813249106 ID - Sims2009 ER - TY - JOUR AU - Jun, S. AU - Sims, G. AU - Wu, G. AU - Kim, S. PY - 2010 DA - 2010// TI - Whole-proteome phylogeny of prokaryotes by feature frequency profiles: an alignment-free method with optimal feature resolution JO - PNAS VL - 107 UR - https://doi.org/10.1073/pnas.0913033107 DO - 10.1073/pnas.0913033107 ID - Jun2010 ER - TY - JOUR AU - Wu, G. AU - Jun, S. AU - Sims, G. AU - Kim, S. PY - 2009 DA - 2009// TI - Whole-proteome phylogeny of large dsDNA virus families by an alignment-free method JO - PNAS VL - 106 UR - https://doi.org/10.1073/pnas.0905115106 DO - 10.1073/pnas.0905115106 ID - Wu2009 ER - TY - JOUR AU - Hao, B. AU - Qi, J. PY - 2004 DA - 2004// TI - Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance JO - J Bioinforma Comput Biol VL - 2 UR - https://doi.org/10.1142/S0219720004000442 DO - 10.1142/S0219720004000442 ID - Hao2004 ER - TY - JOUR AU - Wu, T. AU - Huang, Y. AU - Li, L. PY - 2005 DA - 2005// TI - Optimal word sizes for dissimilarity measures and estimation of the degree of dissimilarity between DNA sequences JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti658 DO - 10.1093/bioinformatics/bti658 ID - Wu2005 ER - TY - JOUR AU - Wu, T. AU - Burke, J. AU - Davison, D. PY - 1997 DA - 1997// TI - A measure of DNA sequence dissimilarity based on the Mahalanobis distance between frequencies of words JO - Biometrics VL - 53 UR - https://doi.org/10.2307/2533509 DO - 10.2307/2533509 ID - Wu1997 ER - TY - JOUR AU - Edgar, R. PY - 2004 DA - 2004// TI - Local homology recognition and distance measures in linear time using compressed amino acid alphabets JO - Bioinformatics VL - 32 ID - Edgar2004 ER - TY - JOUR AU - Van Helden, J. PY - 2004 DA - 2004// TI - Metrics for comparing regulatory sequences on the basis of pattern counts JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/btg425 DO - 10.1093/bioinformatics/btg425 ID - Van Helden2004 ER - TY - JOUR AU - Deerwester, S. AU - Dumais, S. AU - Furnas, W. AU - Landauer, T. AU - Harshman, R. PY - 1990 DA - 1990// TI - Indexing by Latent Semantic Analysis JO - J Am Soc Inf Sci VL - 41 UR - https://doi.org/3.0.CO;2-9 DO - 3.0.CO;2-9 ID - Deerwester1990 ER - TY - JOUR AU - Robinson, D. AU - Foulds, L. PY - 1981 DA - 1981// TI - Comparison 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 - Sokal, R. AU - Rohlf, F. PY - 1962 DA - 1962// TI - The comparison of dendrograms by objective methods JO - Taxon VL - 11 UR - https://doi.org/10.2307/1217208 DO - 10.2307/1217208 ID - Sokal1962 ER - TY - JOUR AU - Nielsen, J. AU - Kristensen, A. AU - Mailund, T. AU - Pedersen, C. PY - 2011 DA - 2011// TI - A sub-cubic time algorithm for computing the quartet distance between two general trees JO - Algoritm Mol Biol VL - 6 UR - https://doi.org/10.1186/1748-7188-6-15 DO - 10.1186/1748-7188-6-15 ID - Nielsen2011 ER - TY - JOUR AU - Hanage, W. AU - Fraser, C. AU - Spratt, B. PY - 2005 DA - 2005// TI - Fuzzy species among recombinogenic bacteria JO - BMC Biol VL - 3 UR - https://doi.org/10.1186/1741-7007-3-6 DO - 10.1186/1741-7007-3-6 ID - Hanage2005 ER - TY - JOUR AU - Escobar-Paramo, P. AU - Giudicelli, C. AU - Parsot, C. AU - Denamur, E. PY - 2003 DA - 2003// TI - The evolutionary history of Shigella and enteroinvasive Escherichia coli revised JO - J Mol Evol VL - 57 UR - https://doi.org/10.1007/s00239-003-2460-3 DO - 10.1007/s00239-003-2460-3 ID - Escobar-Paramo2003 ER - TY - JOUR AU - Ochman, H. AU - Elwyn, S. AU - Moran, N. PY - 1999 DA - 1999// TI - Calibrating bacterial evolution JO - PNAS VL - 96 UR - https://doi.org/10.1073/pnas.96.22.12638 DO - 10.1073/pnas.96.22.12638 ID - Ochman1999 ER - TY - JOUR AU - Yarza, P. AU - Ludwig, W. AU - Euzeby, J. AU - Amann, R. AU - Schleifer, K. -. H. AU - Glockner, F. AU - Rossell-Mra, R. PY - 2010 DA - 2010// TI - Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses JO - Syst Appl Microbiol VL - 33 UR - https://doi.org/10.1016/j.syapm.2010.08.001 DO - 10.1016/j.syapm.2010.08.001 ID - Yarza2010 ER - TY - JOUR AU - Knapp, J. PY - 1988 DA - 1988// TI - Historical perspectives and identification of Neisseria and related species JO - Clin Microbiol Rev VL - 1 UR - https://doi.org/10.1128/CMR.1.4.415 DO - 10.1128/CMR.1.4.415 ID - Knapp1988 ER - TY - JOUR AU - Xu, L. AU - Kuo, J. AU - Liu, J. AU - Wong, T. PY - 2012 DA - 2012// TI - Bacterial phylogenetic tree construction based on genomic translation stop signals JO - Microb Inf Experimentation VL - 2 UR - https://doi.org/10.1186/2042-5783-2-6 DO - 10.1186/2042-5783-2-6 ID - Xu2012 ER - TY - JOUR AU - Vinga, S. AU - Almeida, J. PY - 2003 DA - 2003// TI - Alignment-free sequence comparison - a review JO - 19 VL - 4 ID - Vinga2003 ER - TY - JOUR AU - Tamura, A. AU - Ohashi, N. AU - Urakami, H. AU - Miyanura, S. PY - 1995 DA - 1995// TI - Classification of Rickettsia tsutsugamushi in a New Genus, Orientia gen. nov., as Orientia tsutsugamushi comb. nov JO - Int J Syst Bacteriol VL - 45 UR - https://doi.org/10.1099/00207713-45-3-589 DO - 10.1099/00207713-45-3-589 ID - Tamura1995 ER - TY - JOUR AU - Pfarr, K. AU - Foster, J. AU - Slatko, B. AU - Hoerauf, A. AU - Eisen, J. PY - 2007 DA - 2007// TI - On the taxonomic status of the intracellular bacterium Wolbachia pipientis: should this species name include the intracellular bacteria of filarial nematodes? JO - Int J Syst Evol Microbiol VL - 57 UR - https://doi.org/10.1099/ijs.0.65248-0 DO - 10.1099/ijs.0.65248-0 ID - Pfarr2007 ER - TY - JOUR AU - Garzon, M. AU - Wong, T. PY - 2011 DA - 2011// TI - DNA chips for species identification and biological phylogenies JO - Nat Comput VL - 10 UR - https://doi.org/10.1007/s11047-010-9232-y DO - 10.1007/s11047-010-9232-y ID - Garzon2011 ER - TY - JOUR AU - Ibrahim, A. AU - Goebel, B. AU - Liesack, W. AU - Griffiths, M. AU - Stackebrandt, E. PY - 1993 DA - 1993// TI - The phylogeny of the genus Yersinia based on 16S rDNA sequences JO - FEMS Microbiol Lett VL - 114 UR - https://doi.org/10.1111/j.1574-6968.1993.tb06569.x DO - 10.1111/j.1574-6968.1993.tb06569.x ID - Ibrahim1993 ER - TY - JOUR AU - White, A. AU - Sibley, K. AU - Sibley, C. AU - Wasmuth, J. AU - Schaefer, R. AU - Surette, M. AU - Edge, T. AU - Neumann, N. PY - 2011 DA - 2011// TI - Intergenic sequence comparison of Escherichia coli isolates reveals lifestyle adaptation but not host specificity JO - Appl Environ Microbiol VL - 77 UR - https://doi.org/10.1128/AEM.05909-11 DO - 10.1128/AEM.05909-11 ID - White2011 ER -