메뉴 건너뛰기




Volumn 13, Issue 2, 2006, Pages 336-350

The average common substring approach to phylogenomic reconstruction

Author keywords

Compressibility; Distance matrix; Phylogenomics; Whole genome and proteome phylogeny

Indexed keywords

PROTEOME;

EID: 33646005790     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2006.13.336     Document Type: Conference Paper
Times cited : (183)

References (47)
  • 2
    • 0031721805 scopus 로고    scopus 로고
    • Constructing phylogenies from quartets: Elucidation of eutherian superordinal relationships
    • Ben-Dor, A., Chor, B., Graur, D., Ophir, R., and Pelleg, D. 1998 Constructing phylogenies from quartets: Elucidation of eutherian superordinal relationships. J. Comp. Biol. 5, 377-390.
    • (1998) J. Comp. Biol. , vol.5 , pp. 377-390
    • Ben-Dor, A.1    Chor, B.2    Graur, D.3    Ophir, R.4    Pelleg, D.5
  • 4
    • 0036313785 scopus 로고    scopus 로고
    • Molecular and enzymatic characterization of the porcine endogenous retrovirus protease
    • Blusch, J.H., Seelmeir, S., and Helm, K.V. 2002. Molecular and enzymatic characterization of the porcine endogenous retrovirus protease. Virology 76(15), 7913-7917.
    • (2002) Virology , vol.76 , Issue.15 , pp. 7913-7917
    • Blusch, J.H.1    Seelmeir, S.2    Helm, K.V.3
  • 5
    • 0036143403 scopus 로고    scopus 로고
    • Genome-scale evolution: Reconstructing gene order in ancestral species
    • Bourque, G., and Pevzner, P.A. 2002. Genome-scale evolution: Reconstructing gene order in ancestral species. Genome Res. 12, 26-36.
    • (2002) Genome Res. , vol.12 , pp. 26-36
    • Bourque, G.1    Pevzner, P.A.2
  • 6
    • 0029975554 scopus 로고    scopus 로고
    • The phylogeny of New World (tacaribe complex) arenaviruses
    • Bowen, M.D., Peters, C.J., and Nichol, S.T. 1996. The phylogeny of New World (tacaribe complex) arenaviruses. Virology 219, 285-290.
    • (1996) Virology , vol.219 , pp. 285-290
    • Bowen, M.D.1    Peters, C.J.2    Nichol, S.T.3
  • 7
    • 0036219326 scopus 로고    scopus 로고
    • In silico identification, structure prediction and phylogenetic analysis of the 2′-o-ribose (cap 1) methyltransferase domain in the large structural protein of ssrna negative-strand viruses
    • Bujnicki, J.M., and Rychlewski, L. 2002. In silico identification, structure prediction and phylogenetic analysis of the 2′-o-ribose (cap 1) methyltransferase domain in the large structural protein of ssrna negative-strand viruses. Protein Eng. 15(2), 101-108.
    • (2002) Protein Eng. , vol.15 , Issue.2 , pp. 101-108
    • Bujnicki, J.M.1    Rychlewski, L.2
  • 8
    • 35248890396 scopus 로고    scopus 로고
    • Fast lightweight suffix array construction and checking
    • Baeza-Yates, R. et al., eds., Springer-Verlag, Berlin
    • Burkhardt, S., and Kärkkäinen, J. 2003. Fast lightweight suffix array construction and checking, in Baeza-Yates, R. et al., eds., CPM 2003, LNCS 2676, Springer-Verlag, Berlin.
    • (2003) CPM 2003, LNCS 2676
    • Burkhardt, S.1    Kärkkäinen, J.2
  • 9
    • 0346786316 scopus 로고    scopus 로고
    • New insights into the evolutionary relationships between arenaviruses provided by comparative analysis of small and large segment sequences
    • Charrel, R.N., Lemasson, J.J., Garbutt, M., Khelifa, R., De Micco, P., Feldmann, H., and Lamballerie, de X. 2003. New insights into the evolutionary relationships between arenaviruses provided by comparative analysis of small and large segment sequences. Virology 317, 191-196.
    • (2003) Virology , vol.317 , pp. 191-196
    • Charrel, R.N.1    Lemasson, J.J.2    Garbutt, M.3    Khelifa, R.4    De Micco, P.5    Feldmann, H.6    De Lamballerie, X.7
  • 10
    • 0033691587 scopus 로고    scopus 로고
    • A compression algorithm for DNA sequences and its applications in genome comparison
    • Chen, X., Kwong, S., and Li, M. 2000. A compression algorithm for DNA sequences and its applications in genome comparison. RECOMB '00, 107-117.
    • (2000) RECOMB '00 , pp. 107-117
    • Chen, X.1    Kwong, S.2    Li, M.3
  • 11
    • 26444523116 scopus 로고    scopus 로고
    • Maximum likelihood of evolutionary trees is hard
    • Chor, B., and Tuller, T. 2005. Maximum likelihood of evolutionary trees is hard. RECOMB '05, 296-310.
    • (2005) RECOMB '05 , pp. 296-310
    • Chor, B.1    Tuller, T.2
  • 13
    • 33645960882 scopus 로고    scopus 로고
    • ICTVDB (International Committee on Taxonomy of Viruses Database)
    • Cornelia, B.O. 2002. ICTVDB (International Committee on Taxonomy of Viruses Database). http://phene.cpmc. Columbia.edu/Ictv/index.htm.
    • (2002)
    • Cornelia, B.O.1
  • 16
    • 0002110604 scopus 로고
    • Use of chloroplast DNA rearangements in reconstructing plant phylogeny
    • Soltis, P., Soltis, D., and Doyle, J., eds., Chapman and Hall, London
    • Downie, S., and Palmer, I. 1992. Use of chloroplast DNA rearangements in reconstructing plant phylogeny, in Soltis, P., Soltis, D., and Doyle, J., eds., Plant Molecular Systematics, 14-35, Chapman and Hall, London.
    • (1992) Plant Molecular Systematics , pp. 14-35
    • Downie, S.1    Palmer, I.2
  • 20
    • 0027356277 scopus 로고
    • Molecular biology and evolution of filoviruses
    • Feldmann, H., Klenk, H.D., and Sanchez, A. 1993. Molecular biology and evolution of filoviruses. Arch. Virol. Suppl. 7, 81-100.
    • (1993) Arch. Virol. Suppl. , vol.7 , pp. 81-100
    • Feldmann, H.1    Klenk, H.D.2    Sanchez, A.3
  • 21
    • 0003437299 scopus 로고
    • distributed by the author, Department of Genetics, University of Washington, Seattle
    • Felsenstein, J. 1993. Phylip (Phylogeny Inference Package) Version 3.5c, distributed by the author, Department of Genetics, University of Washington, Seattle.
    • (1993) Phylip (Phylogeny Inference Package) Version 3.5c
    • Felsenstein, J.1
  • 22
    • 0001807019 scopus 로고
    • Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals)
    • Hannenhalli, S., and Pevzner, P. 1995. Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). Proc. 27th Ann. ACM Symp. on the Theory of Computing, 178-189.
    • (1995) Proc. 27th Ann. ACM Symp. on the Theory of Computing , pp. 178-189
    • Hannenhalli, S.1    Pevzner, P.2
  • 23
    • 0842325992 scopus 로고    scopus 로고
    • Complete genome sequence of fer-de-lance virus reveals a novel gene in reptilian paramyxoviruses
    • Kurath, G., Batts, W.N., Ahne, W., and Winton, J.R. 2004. Complete genome sequence of fer-de-lance virus reveals a novel gene in reptilian paramyxoviruses. J. Virology 78(4), 2045-2056.
    • (2004) J. Virology , vol.78 , Issue.4 , pp. 2045-2056
    • Kurath, G.1    Batts, W.N.2    Ahne, W.3    Winton, J.R.4
  • 24
    • 0016880887 scopus 로고
    • On the complexity of finite sequences
    • Lempel, A., and Ziv, J. 1976. On the complexity of finite sequences. IEEE Trans. Inf. Theory 22, 75-88.
    • (1976) IEEE Trans. Inf. Theory , vol.22 , pp. 75-88
    • Lempel, A.1    Ziv, J.2
  • 25
    • 0017493286 scopus 로고
    • A universal algorithm for sequential data compression
    • Lempel A., and Ziv, J. 1977. A universal algorithm for sequential data compression. IEEE Trans. Inf. Theory 23(3), 337-343.
    • (1977) IEEE Trans. Inf. Theory , vol.23 , Issue.3 , pp. 337-343
    • Lempel, A.1    Ziv, J.2
  • 26
    • 0035102453 scopus 로고    scopus 로고
    • An information-based sequence distance and its application to whole mitochondrial genome phylogeny
    • Li, M., Badger, J., Chen, X., Kwong, S., Kearney, P., and Zhang, H. 2001. An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics 17(2), 149-154.
    • (2001) Bioinformatics , vol.17 , Issue.2 , pp. 149-154
    • Li, M.1    Badger, J.2    Chen, X.3    Kwong, S.4    Kearney, P.5    Zhang, H.6
  • 27
    • 0034938644 scopus 로고    scopus 로고
    • From gene trees to species trees
    • Ma, B., Li, M., and Zhang, L. 2000. From gene trees to species trees. SIAM J. Comp. 30(3), 729-752.
    • (2000) SIAM J. Comp. , vol.30 , Issue.3 , pp. 729-752
    • Ma, B.1    Li, M.2    Zhang, L.3
  • 29
    • 0346786312 scopus 로고    scopus 로고
    • Full-length genome sequence of mossman virus, a novel paramyxovirus isolated from rodents in Australia
    • Miller, P.J., Boyle, D.B., Eaton, B.T., and Wang, L. 2003. Full-length genome sequence of mossman virus, a novel paramyxovirus isolated from rodents in Australia. Virology 317, 330-334.
    • (2003) Virology , vol.317 , pp. 330-334
    • Miller, P.J.1    Boyle, D.B.2    Eaton, B.T.3    Wang, L.4
  • 30
    • 0035229986 scopus 로고    scopus 로고
    • New approaches for reconstructing phylogenies from gene order data
    • Moret, B.M.E., Wang, L.S., Warnow, T., and Wyman, S.K. 2001. New approaches for reconstructing phylogenies from gene order data. Bioinformatics 17, 165-173.
    • (2001) Bioinformatics , vol.17 , pp. 165-173
    • Moret, B.M.E.1    Wang, L.S.2    Warnow, T.3    Wyman, S.K.4
  • 31
    • 33645961190 scopus 로고    scopus 로고
    • NCBI Genome Entrez. 2005. www.ncbi.nlm.nih.gov/entrez/query.fcgi?db= genome.
    • (2005)
  • 33
    • 0242643741 scopus 로고    scopus 로고
    • A new sequence distance measure for phylogenetic tree construction
    • Otu, H.H., and Sayood, K. 2003. A new sequence distance measure for phylogenetic tree construction. Bioinformatics 19(16).
    • (2003) Bioinformatics , vol.19 , Issue.16
    • Otu, H.H.1    Sayood, K.2
  • 34
    • 1242335920 scopus 로고    scopus 로고
    • Whole proteome prokaryote phylogeny without sequence alignment: A k-string composition approach
    • Qi, J., Wang, B., and Hao, B. 2004. Whole proteome prokaryote phylogeny without sequence alignment: A k-string composition approach. J. Mol. Evol. 58(1), 1-11.
    • (2004) J. Mol. Evol. , vol.58 , Issue.1 , pp. 1-11
    • Qi, J.1    Wang, B.2    Hao, B.3
  • 36
    • 0034117084 scopus 로고    scopus 로고
    • Where do rodents fit? Evidence from the complete mitochondrial genome of Sciurus vulgaris
    • Reyes, A., Gissi, C., Pesole, G., Catzeflis, P.M., and Saccone, C. 2000. Where do rodents fit? Evidence from the complete mitochondrial genome of Sciurus vulgaris. Mol. Biol. Evol. 17, 979-983.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 979-983
    • Reyes, A.1    Gissi, C.2    Pesole, G.3    Catzeflis, P.M.4    Saccone, C.5
  • 37
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • Robinson, D.R., and Foulds, L.R. 1981. Comparison of phylogenetic trees. Math. Biosci. 53, 131-147.
    • (1981) Math. Biosci. , vol.53 , pp. 131-147
    • Robinson, D.R.1    Foulds, L.R.2
  • 39
    • 0033982962 scopus 로고    scopus 로고
    • Avian endogenous retrovirus eav-hp shares regions of identity with avian leukosis virus subgroup j and the avian retrotransposon art-ch
    • Sacco, M.A., Flannery, D.M.J., Howes, K., and Venugopal, K. 2000. Avian endogenous retrovirus eav-hp shares regions of identity with avian leukosis virus subgroup j and the avian retrotransposon art-ch. J. Virology 74(3), 1296-1306.
    • (2000) J. Virology , vol.74 , Issue.3 , pp. 1296-1306
    • Sacco, M.A.1    Flannery, D.M.J.2    Howes, K.3    Venugopal, K.4
  • 40
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou, N., and Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 42
    • 4043169069 scopus 로고    scopus 로고
    • A comprehensive whole genome bacterial phylogeny using correlated peptide motive defined in a high dimensional vector space
    • Stuart, G.W., and Berry, M.W. 2003. A comprehensive whole genome bacterial phylogeny using correlated peptide motive defined in a high dimensional vector space. J. Bioinf. Comp. Biol. 1(3), 475-493.
    • (2003) J. Bioinf. Comp. Biol. , vol.1 , Issue.3 , pp. 475-493
    • Stuart, G.W.1    Berry, M.W.2
  • 43
    • 0035144177 scopus 로고    scopus 로고
    • Sequence comparison of an Australian duck hepatitis b virus strain with other avian hepadnaviruses
    • Triyatnib, M., Ey, PL., Tran, T., Mire, M.L., Qiao, M., Burrell, C.J., and Jilbert, A.R. 2001. Sequence comparison of an Australian duck hepatitis b virus strain with other avian hepadnaviruses. J. Gen. Virology 82, 373-378.
    • (2001) J. Gen. Virology , vol.82 , pp. 373-378
    • Triyatnib, M.1    Ey, P.L.2    Tran, T.3    Mire, M.L.4    Qiao, M.5    Burrell, C.J.6    Jilbert, A.R.7
  • 46
    • 0029307103 scopus 로고
    • Improved redundancy of a version of the Lempel-Ziv algorithm
    • Wyner, A.D., and Wyner, A.J. 1995. Improved redundancy of a version of the Lempel-Ziv algorithm. IEEE Trans. Inform. Theory 41(3), 723-731.
    • (1995) IEEE Trans. Inform. Theory , vol.41 , Issue.3 , pp. 723-731
    • Wyner, A.D.1    Wyner, A.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.