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Volumn 13, Issue 1, 2012, Pages

Detection of horizontal transfer of individual genes by anomalous oligomer frequencies

Author keywords

[No Author keywords available]

Indexed keywords

OLIGOMER;

EID: 84862201625     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-245     Document Type: Article
Times cited : (6)

References (64)
  • 1
    • 57149085868 scopus 로고    scopus 로고
    • Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world
    • 10.1093/nar/gkn668, 2588523, 18948295
    • Koonin EV, Wolf YI. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res 2008, 36:6688-6719. 10.1093/nar/gkn668, 2588523, 18948295.
    • (2008) Nucleic Acids Res , vol.36 , pp. 6688-6719
    • Koonin, E.V.1    Wolf, Y.I.2
  • 2
    • 3042849253 scopus 로고    scopus 로고
    • Biased biological functions of horizontally transferred genes in prokaryotic genomes
    • 10.1038/ng1381, 15208628
    • Nakamura Y, Itoh T, Matsuda H, Gojobori T. Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat Genet 2004, 36:760-766. 10.1038/ng1381, 15208628.
    • (2004) Nat Genet , vol.36 , pp. 760-766
    • Nakamura, Y.1    Itoh, T.2    Matsuda, H.3    Gojobori, T.4
  • 3
    • 67651011811 scopus 로고    scopus 로고
    • Lateral genetic transfer: open issues
    • 10.1098/rstb.2009.0031, 2872999, 19571244
    • Ragan MA, Beiko RG. Lateral genetic transfer: open issues. Phil Trans R Soc B 2009, 364:2241-2251. 10.1098/rstb.2009.0031, 2872999, 19571244.
    • (2009) Phil Trans R Soc B , vol.364 , pp. 2241-2251
    • Ragan, M.A.1    Beiko, R.G.2
  • 4
    • 77957743043 scopus 로고    scopus 로고
    • Eradicating typological thinking in prokaryotic systematics and evolution
    • 10.1101/sqb.2009.74.002, 19667014
    • Doolittle WF. Eradicating typological thinking in prokaryotic systematics and evolution. Cold Spring Harbor Symp Quant Biol 2009, 74:197-204. 10.1101/sqb.2009.74.002, 19667014.
    • (2009) Cold Spring Harbor Symp Quant Biol , vol.74 , pp. 197-204
    • Doolittle, W.F.1
  • 5
    • 0028606283 scopus 로고
    • Horizontal gene transfer: evidence and possible consequences
    • 10.1146/annurev.ge.28.120194.001321, 7893125
    • Syvanen M. Horizontal gene transfer: evidence and possible consequences. Annu Rev Genet 1994, 28:237-261. 10.1146/annurev.ge.28.120194.001321, 7893125.
    • (1994) Annu Rev Genet , vol.28 , pp. 237-261
    • Syvanen, M.1
  • 6
    • 0035099964 scopus 로고    scopus 로고
    • Codon bias and base composition are poor indicators of horizontally transferred genes
    • 10.1093/oxfordjournals.molbev.a003816, 11230541
    • Koski LB, Morton RA, Golding GB. Codon bias and base composition are poor indicators of horizontally transferred genes. Mol Biol Evol 2001, 18:404-412. 10.1093/oxfordjournals.molbev.a003816, 11230541.
    • (2001) Mol Biol Evol , vol.18 , pp. 404-412
    • Koski, L.B.1    Morton, R.A.2    Golding, G.B.3
  • 7
    • 0036145420 scopus 로고    scopus 로고
    • Reconciling the many faces of lateral gene transfer
    • 10.1016/S0966-842X(01)02282-X, 11755071
    • Lawrence JG, Ochman H. Reconciling the many faces of lateral gene transfer. Trends Microbiol 2002, 10:1-4. 10.1016/S0966-842X(01)02282-X, 11755071.
    • (2002) Trends Microbiol , vol.10 , pp. 1-4
    • Lawrence, J.G.1    Ochman, H.2
  • 8
    • 34047234772 scopus 로고    scopus 로고
    • The power of phylogenetic approaches to detect horizontally transferred genes
    • 10.1186/1471-2148-7-45, 1847511, 17376230
    • Poptsova MS, Gogarten JP. The power of phylogenetic approaches to detect horizontally transferred genes. BMC Evol Biol 2007, 7:45. 10.1186/1471-2148-7-45, 1847511, 17376230.
    • (2007) BMC Evol Biol , vol.7 , pp. 45
    • Poptsova, M.S.1    Gogarten, J.P.2
  • 9
    • 0033670249 scopus 로고    scopus 로고
    • Horizontal Gene Transfer in Bacterial and Archaeal Complete Genomes
    • 10.1101/gr.130000, 310969, 11076857
    • Garcia-Vallvé S, Romeu A, Palau J. Horizontal Gene Transfer in Bacterial and Archaeal Complete Genomes. Genome Res 2000, 10:1719-1725. 10.1101/gr.130000, 310969, 11076857.
    • (2000) Genome Res , vol.10 , pp. 1719-1725
    • Garcia-Vallvé, S.1    Romeu, A.2    Palau, J.3
  • 10
    • 0026332291 scopus 로고
    • Evidence for horizontal gene transfer in Escherichia coli speciation
    • Médigue C, Rouxel T, Vigier P, Hénaut A, Danchin A. Evidence for horizontal gene transfer in Escherichia coli speciation. J Mol Biol 1991, 222:651-656.
    • (1991) J Mol Biol , vol.222 , pp. 651-656
    • Médigue, C.1    Rouxel, T.2    Vigier, P.3    Hénaut, A.4    Danchin, A.5
  • 11
    • 0035312272 scopus 로고    scopus 로고
    • Highly expressed and alien genes of the Synechocystis genome
    • Mrázek J, Bhaya D, Grossman AR, Karlin S. Highly expressed and alien genes of the Synechocystis genome. Nucleic Acids Res 2002, 29:1590-1601.
    • (2002) Nucleic Acids Res , vol.29 , pp. 1590-1601
    • Mrázek, J.1    Bhaya, D.2    Grossman, A.R.3    Karlin, S.4
  • 12
    • 0030994798 scopus 로고    scopus 로고
    • Amelioration of bacterial genomes: rates of change and exchange
    • 10.1007/PL00006158, 9089078
    • Lawrence JG, Ochman H. Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 1997, 44:383-397. 10.1007/PL00006158, 9089078.
    • (1997) J Mol Evol , vol.44 , pp. 383-397
    • Lawrence, J.G.1    Ochman, H.2
  • 13
    • 0034887748 scopus 로고    scopus 로고
    • Capturing whole-genome characteristics in short sequences using a naïve Bayesian classifier
    • 10.1101/gr.186401, 311094, 11483581
    • Sandberg R, Winberg G, Bränden C-I, Kaske A, Ernberg I, Cöster J. Capturing whole-genome characteristics in short sequences using a naïve Bayesian classifier. Genome Res 2001, 11:1404-1409. 10.1101/gr.186401, 311094, 11483581.
    • (2001) Genome Res , vol.11 , pp. 1404-1409
    • Sandberg, R.1    Winberg, G.2    Bränden, C.-I.3    Kaske, A.4    Ernberg, I.5    Cöster, J.6
  • 14
    • 3042849253 scopus 로고    scopus 로고
    • Biased biological functions of horizontally transferred genes in prokaryotic genomes
    • 10.1038/ng1381, 15208628
    • Nakamura Y, Itoh T, Matsuda H, Gojobori T. Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nature Genet 2004, 36:760-766. 10.1038/ng1381, 15208628.
    • (2004) Nature Genet , vol.36 , pp. 760-766
    • Nakamura, Y.1    Itoh, T.2    Matsuda, H.3    Gojobori, T.4
  • 15
    • 19744383764 scopus 로고    scopus 로고
    • Detection and characterization of horizontal transfers in prokaryotes using genomic signature
    • Dufraigne C, Fertil B, Lespinats S, Giron A, Deschavanne P. Detection and characterization of horizontal transfers in prokaryotes using genomic signature. NucleicAcids Res 2005, 33:e6.
    • (2005) NucleicAcids Res , vol.33
    • Dufraigne, C.1    Fertil, B.2    Lespinats, S.3    Giron, A.4    Deschavanne, P.5
  • 16
    • 13944251386 scopus 로고    scopus 로고
    • A new computational method for the detection of horizontal gene transfer events
    • 10.1093/nar/gki187, 549390, 15716310
    • Tsirigos A, Rigoutsos I. A new computational method for the detection of horizontal gene transfer events. Nucleic Acids Res 2005, 33:922-933. 10.1093/nar/gki187, 549390, 15716310.
    • (2005) Nucleic Acids Res , vol.33 , pp. 922-933
    • Tsirigos, A.1    Rigoutsos, I.2
  • 17
    • 33748689309 scopus 로고    scopus 로고
    • Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands
    • 10.1093/bioinformatics/btl369, 16837528
    • Vernikos GS, Parkhill J. Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 2006, 22:2196-2203. 10.1093/bioinformatics/btl369, 16837528.
    • (2006) Bioinformatics , vol.22 , pp. 2196-2203
    • Vernikos, G.S.1    Parkhill, J.2
  • 18
    • 38849113877 scopus 로고    scopus 로고
    • Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patterns
    • Zaneveld JR, Nernergut DR, Knight R. Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patterns. Microbiol 2008, 154:1-15.
    • (2008) Microbiol , vol.154 , pp. 1-15
    • Zaneveld, J.R.1    Nernergut, D.R.2    Knight, R.3
  • 19
    • 0035943134 scopus 로고    scopus 로고
    • On surrogate methods for detecting lateral gene transfer
    • 10.1111/j.1574-6968.2001.tb10755.x, 11470360
    • Ragan MR. On surrogate methods for detecting lateral gene transfer. FEMS Microbiol Lett 2001, 201:187-191. 10.1111/j.1574-6968.2001.tb10755.x, 11470360.
    • (2001) FEMS Microbiol Lett , vol.201 , pp. 187-191
    • Ragan, M.R.1
  • 20
    • 30344471824 scopus 로고    scopus 로고
    • Do different surrogate methods detect lateral genetic transfer events of different relative ages?
    • 10.1016/j.tim.2005.11.004, 16356716
    • Ragan MR, Harlow TJ, Beiko RG. Do different surrogate methods detect lateral genetic transfer events of different relative ages?. Trends Microbiol 2006, 14:4-8. 10.1016/j.tim.2005.11.004, 16356716.
    • (2006) Trends Microbiol , vol.14 , pp. 4-8
    • Ragan, M.R.1    Harlow, T.J.2    Beiko, R.G.3
  • 21
    • 55449123112 scopus 로고    scopus 로고
    • Use of artificial genomes in assessing methods for atypical gene detection
    • 10.1371/journal.pcbi.0010056, 1282332, 16292353
    • Azad RK, Lawrence JG. Use of artificial genomes in assessing methods for atypical gene detection. PloS Comput Biol 2005, 1:e56. 10.1371/journal.pcbi.0010056, 1282332, 16292353.
    • (2005) PloS Comput Biol , vol.1
    • Azad, R.K.1    Lawrence, J.G.2
  • 22
    • 10944248427 scopus 로고    scopus 로고
    • Computing prokaryotic gene ubiquity: Rescuing the core from extinction
    • 10.1101/gr.3024704, 534671, 15574825
    • Charlebois RL, Doolittle RF. Computing prokaryotic gene ubiquity: Rescuing the core from extinction. Genome Res 2004, 14:2469-2477. 10.1101/gr.3024704, 534671, 15574825.
    • (2004) Genome Res , vol.14 , pp. 2469-2477
    • Charlebois, R.L.1    Doolittle, R.F.2
  • 23
    • 0030740993 scopus 로고    scopus 로고
    • Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes
    • 10.1093/nar/25.12.2430, 1995031, 9171096
    • Gelfand MS, Koonin EV. Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes. Nucleic Acids Res 1997, 25:2430-2439. 10.1093/nar/25.12.2430, 1995031, 9171096.
    • (1997) Nucleic Acids Res , vol.25 , pp. 2430-2439
    • Gelfand, M.S.1    Koonin, E.V.2
  • 24
    • 0141459098 scopus 로고    scopus 로고
    • Distribution of potential type II restriction sites (palindromes) in prokaryotes
    • 10.1016/j.bbrc.2003.09.014, 14521907
    • Fuglsang A. Distribution of potential type II restriction sites (palindromes) in prokaryotes. Biochem Biophys Res Commun 2003, 310:280-285. 10.1016/j.bbrc.2003.09.014, 14521907.
    • (2003) Biochem Biophys Res Commun , vol.310 , pp. 280-285
    • Fuglsang, A.1
  • 25
    • 0035883519 scopus 로고    scopus 로고
    • Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution
    • 10.1093/nar/29.18.3742, 55917, 11557807
    • Kobayashi I. Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res 2001, 29:3742-3756. 10.1093/nar/29.18.3742, 55917, 11557807.
    • (2001) Nucleic Acids Res , vol.29 , pp. 3742-3756
    • Kobayashi, I.1
  • 28
    • 0035707917 scopus 로고    scopus 로고
    • An overview of the genome of Nostoc punctiforme, a multicellular, symbiotic cyanobacterium
    • 10.1023/A:1013840025518, 16228364
    • Meeks JC, Elhai J, Thiel T, Potts M, Larimer F, Lamerdin J, Predki P, Atlas R. An overview of the genome of Nostoc punctiforme, a multicellular, symbiotic cyanobacterium. Photosynth Res 2001, 70:85-106. 10.1023/A:1013840025518, 16228364.
    • (2001) Photosynth Res , vol.70 , pp. 85-106
    • Meeks, J.C.1    Elhai, J.2    Thiel, T.3    Potts, M.4    Larimer, F.5    Lamerdin, J.6    Predki, P.7    Atlas, R.8
  • 36
    • 24944486210 scopus 로고    scopus 로고
    • High-throughput functional analysis of the Synechococcus elongatus PCC 7942 genome
    • 10.1093/dnares/12.2.103, 16303742
    • Holtman CK, Chen Y, Sandoval P, Gonzales A, Nalty MS, Thomas TL, Youderian P, Golden SS. High-throughput functional analysis of the Synechococcus elongatus PCC 7942 genome. DNA Res 2005, 12:103-115. 10.1093/dnares/12.2.103, 16303742.
    • (2005) DNA Res , vol.12 , pp. 103-115
    • Holtman, C.K.1    Chen, Y.2    Sandoval, P.3    Gonzales, A.4    Nalty, M.S.5    Thomas, T.L.6    Youderian, P.7    Golden, S.S.8
  • 40
    • 0032509302 scopus 로고    scopus 로고
    • Genome sequence of the nematode C. elegans: A platform for investigating biology
    • The C. elegans Sequencing Consortium
    • The C. elegans Sequencing Consortium Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 1998, 282:2012-2018. The C. elegans Sequencing Consortium.
    • (1998) Science , vol.282 , pp. 2012-2018
  • 41
    • 0028968327 scopus 로고
    • Singular over-representation of an octameric palindrome, HIP1, in DNA from many cyanobacteria
    • 10.1093/nar/23.5.729, 306751, 7708486
    • Robinson NJ, Robinson PJ, Gupta A, Bleasby AJ, Whitton BA, Morby AP. Singular over-representation of an octameric palindrome, HIP1, in DNA from many cyanobacteria. Nucleic Acids Res 1995, 23:729-735. 10.1093/nar/23.5.729, 306751, 7708486.
    • (1995) Nucleic Acids Res , vol.23 , pp. 729-735
    • Robinson, N.J.1    Robinson, P.J.2    Gupta, A.3    Bleasby, A.J.4    Whitton, B.A.5    Morby, A.P.6
  • 42
    • 33748277982 scopus 로고    scopus 로고
    • Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events
    • 10.1101/gr.5322306, 1557764, 16899658
    • Zhaxybayeva O, Gogarten JP, Charlebois RL, Doolittle WF, Papke RT. Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Res 2006, 16:1099-1108. 10.1101/gr.5322306, 1557764, 16899658.
    • (2006) Genome Res , vol.16 , pp. 1099-1108
    • Zhaxybayeva, O.1    Gogarten, J.P.2    Charlebois, R.L.3    Doolittle, W.F.4    Papke, R.T.5
  • 43
    • 65549147805 scopus 로고    scopus 로고
    • Microbial co-habitation and lateral gene transfer: what transposases can tell us
    • 10.1186/gb-2009-10-4-r45, 2688936, 19393086
    • Hooper SD, Mavromatis K, Kyrpides NC. Microbial co-habitation and lateral gene transfer: what transposases can tell us. Genome Biol 2009, 10:R45. 10.1186/gb-2009-10-4-r45, 2688936, 19393086.
    • (2009) Genome Biol , vol.10
    • Hooper, S.D.1    Mavromatis, K.2    Kyrpides, N.C.3
  • 45
    • 0042027842 scopus 로고    scopus 로고
    • Phylogenetics and the cohesion of bacterial genomes
    • 10.1126/science.1086568, 12907801
    • Daubin V, Moran NA, Ochman H. Phylogenetics and the cohesion of bacterial genomes. Science 2003, 301:829-832. 10.1126/science.1086568, 12907801.
    • (2003) Science , vol.301 , pp. 829-832
    • Daubin, V.1    Moran, N.A.2    Ochman, H.3
  • 46
    • 0034882455 scopus 로고    scopus 로고
    • Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes
    • 10.1093/oxfordjournals.molbev.a003972, 11504864
    • Guindon S, Perrière G. Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes. Molec Biol Evol 2001, 18:1838-1840. 10.1093/oxfordjournals.molbev.a003972, 11504864.
    • (2001) Molec Biol Evol , vol.18 , pp. 1838-1840
    • Guindon, S.1    Perrière, G.2
  • 47
    • 0032517137 scopus 로고    scopus 로고
    • Skewed oligomers and origins of replication
    • 10.1016/S0378-1119(98)00374-6, 9795135
    • Salzberg SL, Salzberg AJ, Kerlavage AR, Tomb J-F. Skewed oligomers and origins of replication. Gene 1998, 217:57-67. 10.1016/S0378-1119(98)00374-6, 9795135.
    • (1998) Gene , vol.217 , pp. 57-67
    • Salzberg, S.L.1    Salzberg, A.J.2    Kerlavage, A.R.3    Tomb, J.-F.4
  • 48
    • 0033374593 scopus 로고    scopus 로고
    • Characteristics of Chi distribution on different bacterial genomes
    • 10.1016/S0923-2508(99)00132-1, 10672998
    • El Karoui M, Biaudet V, Schbath S, Gruss A. Characteristics of Chi distribution on different bacterial genomes. Res Microbiol 1999, 150:579-587. 10.1016/S0923-2508(99)00132-1, 10672998.
    • (1999) Res Microbiol , vol.150 , pp. 579-587
    • El Karoui, M.1    Biaudet, V.2    Schbath, S.3    Gruss, A.4
  • 49
    • 77957697198 scopus 로고    scopus 로고
    • Coevolution of DNA uptake sequences and bacterial proteomes
    • 2817400, 20333176
    • Findlay WA, Redfield RJ. Coevolution of DNA uptake sequences and bacterial proteomes. Genome Biol Evol 2009, 1:45-55. 2817400, 20333176.
    • (2009) Genome Biol Evol , vol.1 , pp. 45-55
    • Findlay, W.A.1    Redfield, R.J.2
  • 50
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: improvement in accuracy of multiple sequence alignment
    • 10.1093/nar/gki198, 548345, 15661851
    • Katoh K, Kuma K-I, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 2005, 33:511-518. 10.1093/nar/gki198, 548345, 15661851.
    • (2005) Nucleic Acids Res , vol.33 , pp. 511-518
    • Katoh, K.1    Kuma, K.-I.2    Toh, H.3    Miyata, T.4
  • 51
    • 33747847779 scopus 로고    scopus 로고
    • PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
    • 1538804, 16845082
    • Suyama M, Torrents D, Bork P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 2006, 34(suppl. 2):W609-W612. 1538804, 16845082.
    • (2006) Nucleic Acids Res , vol.34 , Issue.SUPPL. 2
    • Suyama, M.1    Torrents, D.2    Bork, P.3
  • 52
    • 34547489084 scopus 로고    scopus 로고
    • Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
    • 10.1080/10635150701472164, 17654362
    • Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 2007, 56:564-577. 10.1080/10635150701472164, 17654362.
    • (2007) Syst Biol , vol.56 , pp. 564-577
    • Talavera, G.1    Castresana, J.2
  • 53
    • 38649110663 scopus 로고    scopus 로고
    • BEAST: Bayesian evolutionary analysis by sampling trees
    • 10.1186/1471-2148-7-214, 2247476, 17996036
    • Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 2007, 7:214. 10.1186/1471-2148-7-214, 2247476, 17996036.
    • (2007) BMC Evol Biol , vol.7 , pp. 214
    • Drummond, A.J.1    Rambaut, A.2
  • 54
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • 10.1080/10635150390235520, 14530136
    • Guindon S, Gascuel OA. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003, 52:696-704. 10.1080/10635150390235520, 14530136.
    • (2003) Syst Biol , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.A.2
  • 55
    • 1642341403 scopus 로고    scopus 로고
    • Bayesian phylogenetic analysis of combined data
    • 10.1080/10635150490264699, 14965900
    • Nylander JA, Ronquist F, Huelsenbeck JP, Nieves-Aldrey JL. Bayesian phylogenetic analysis of combined data. Syst Biol 2004, 53:47-67. 10.1080/10635150490264699, 14965900.
    • (2004) Syst Biol , vol.53 , pp. 47-67
    • Nylander, J.A.1    Ronquist, F.2    Huelsenbeck, J.P.3    Nieves-Aldrey, J.L.4
  • 57
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • 10.1093/nar/25.17.3389, 146917, 9254694
    • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schäffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 58
    • 0023650543 scopus 로고
    • The Codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications
    • 10.1093/nar/15.3.1281, 340524, 3547335
    • Sharp PM, Li WH. The Codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 1987, 15:1281-1295. 10.1093/nar/15.3.1281, 340524, 3547335.
    • (1987) Nucleic Acids Res , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 60
    • 0000122573 scopus 로고
    • PHYLIP - Phylogeny Inference Package (Version 3.2)
    • Felsenstein J. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 1989, 5:164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 62
    • 0036205377 scopus 로고    scopus 로고
    • TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing
    • 10.1093/bioinformatics/18.3.502, 11934758
    • Schmidt HA, Strimmer K, Vingron M, von Haeseler A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 2002, 18:502-504. 10.1093/bioinformatics/18.3.502, 11934758.
    • (2002) Bioinformatics , vol.18 , pp. 502-504
    • Schmidt, H.A.1    Strimmer, K.2    Vingron, M.3    von Haeseler, A.4
  • 63
    • 0029836454 scopus 로고    scopus 로고
    • Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies
    • Strimmer K, von Haeseler A. Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies. Mol Biol Evol 1996, 13:964-969.
    • (1996) Mol Biol Evol , vol.13 , pp. 964-969
    • Strimmer, K.1    von Haeseler, A.2
  • 64
    • 0021277009 scopus 로고
    • A new method for calculating evolutionary substitution rates
    • 10.1007/BF02101990, 6429346
    • Lanave C, Preparata G, Saccone C, Serio G. A new method for calculating evolutionary substitution rates. J Mol Evol 1984, 20:86-93. 10.1007/BF02101990, 6429346.
    • (1984) J Mol Evol , vol.20 , pp. 86-93
    • Lanave, C.1    Preparata, G.2    Saccone, C.3    Serio, G.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.