메뉴 건너뛰기




Volumn 14, Issue , 2013, Pages

TPMS: A set of utilities for querying collections of gene trees

Author keywords

[No Author keywords available]

Indexed keywords

COLLECTION BUILDING; COMPARATIVE GENOMIC; COMPLEX PATTERN; PHYLOGENETIC TREES; RIGOROUS APPROACH; SEARCH STRATEGIES; SEQUENCE ANALYSIS; SYSTEMATIC SEARCHES;

EID: 84875303091     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-109     Document Type: Article
Times cited : (4)

References (27)
  • 1
    • 20744436518 scopus 로고    scopus 로고
    • Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases
    • 10.1093/bioinformatics/bti325, 15713731
    • Dufayard JF, Duret L, Penel S, Gouy M, Rechenmann F, Perrière G. Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics 2005, 21:2596-2603. 10.1093/bioinformatics/bti325, 15713731.
    • (2005) Bioinformatics , vol.21 , pp. 2596-2603
    • Dufayard, J.F.1    Duret, L.2    Penel, S.3    Gouy, M.4    Rechenmann, F.5    Perrière, G.6
  • 2
    • 74049118261 scopus 로고    scopus 로고
    • Large-scale assignment of orthology: back to phylogenetics?
    • 10.1186/gb-2008-9-10-235, 2760865, 18983710
    • Gabaldón T. Large-scale assignment of orthology: back to phylogenetics?. Genome Biol 2008, 9:235. 10.1186/gb-2008-9-10-235, 2760865, 18983710.
    • (2008) Genome Biol , vol.9 , pp. 235
    • Gabaldón, T.1
  • 3
    • 59149102602 scopus 로고    scopus 로고
    • Phylogenetic and functional assessment of orthologs inference projects and methods
    • 10.1371/journal.pcbi.1000262, 2612752, 19148271
    • Altenhoff AM, Dessimoz C. Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol 2009, 5:e1000262. 10.1371/journal.pcbi.1000262, 2612752, 19148271.
    • (2009) PLoS Comput Biol , vol.5
    • Altenhoff, A.M.1    Dessimoz, C.2
  • 4
    • 78651277241 scopus 로고    scopus 로고
    • MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score
    • 3061081, 21149260
    • Pryszcz LP, Huerta-Cepas J, Gabaldón T. MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score. Nucleic Acids Res 2010, 39:e32. 3061081, 21149260.
    • (2010) Nucleic Acids Res , vol.39
    • Pryszcz, L.P.1    Huerta-Cepas, J.2    Gabaldón, T.3
  • 5
    • 77954843377 scopus 로고    scopus 로고
    • Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests
    • 10.1186/1471-2105-11-324, 2905365, 20550700
    • Abby SS, Tannier E, Gouy M, Daubin V. Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. BMC Bioinformatics 2010, 11:324. 10.1186/1471-2105-11-324, 2905365, 20550700.
    • (2010) BMC Bioinformatics , vol.11 , pp. 324
    • Abby, S.S.1    Tannier, E.2    Gouy, M.3    Daubin, V.4
  • 6
    • 50649104620 scopus 로고    scopus 로고
    • Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes
    • 10.1101/gr.076992.108, 2527703, 18562677
    • Studer RA, Penel S, Duret L, Robinson-Rechavi M. Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. Genome Res 2008, 18:1393-1402. 10.1101/gr.076992.108, 2527703, 18562677.
    • (2008) Genome Res , vol.18 , pp. 1393-1402
    • Studer, R.A.1    Penel, S.2    Duret, L.3    Robinson-Rechavi, M.4
  • 7
    • 17244367011 scopus 로고    scopus 로고
    • Homology-dependent methylation in primate repetitive DNA
    • 10.1073/pnas.0408986102, 556223, 15797989
    • Meunier J, Khelifi A, Navratil V, Duret L. Homology-dependent methylation in primate repetitive DNA. Proc Natl Acad Sci USA 2005, 102:5471-5476. 10.1073/pnas.0408986102, 556223, 15797989.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 5471-5476
    • Meunier, J.1    Khelifi, A.2    Navratil, V.3    Duret, L.4
  • 8
    • 2942684863 scopus 로고    scopus 로고
    • The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny
    • 10.1007/s00239-004-2587-x, 15461422
    • Belle EM, Duret L, Galtier N, Eyre-Walker A. The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny. J Mol Evol 2004, 58:653-660. 10.1007/s00239-004-2587-x, 15461422.
    • (2004) J Mol Evol , vol.58 , pp. 653-660
    • Belle, E.M.1    Duret, L.2    Galtier, N.3    Eyre-Walker, A.4
  • 10
    • 33745955637 scopus 로고    scopus 로고
    • Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics
    • 10.1186/1471-2105-7-188, 1501049, 16594991
    • Dutheil J, Gaillard S, Bazin E, Glemin S, Ranwez V, Galtier N, Belkhir K. Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics. BMC Bioinformatics 2006, 7:188. 10.1186/1471-2105-7-188, 1501049, 16594991.
    • (2006) BMC Bioinformatics , vol.7 , pp. 188
    • Dutheil, J.1    Gaillard, S.2    Bazin, E.3    Glemin, S.4    Ranwez, V.5    Galtier, N.6    Belkhir, K.7
  • 11
    • 84864346710 scopus 로고    scopus 로고
    • Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny
    • 10.1098/rspb.2012.0683, 22628470, Yang Z
    • Dos Reis M, Inoue J, Hasegawa M, Asher RJ, Donoghue PCJ, Yang Z Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc R Soc B 2012, 279:3491-3500. 10.1098/rspb.2012.0683, 22628470, Yang Z.
    • (2012) Proc R Soc B , vol.279 , pp. 3491-3500
    • Dos Reis, M.1    Inoue, J.2    Hasegawa, M.3    Asher, R.J.4    Donoghue, P.C.J.5
  • 12
    • 0033759527 scopus 로고    scopus 로고
    • The comparison of beta-thymosin homologues among metazoa supports an arthropod-nematode clade
    • Manuel M, Kruse M, Muller WE, Le Parco Y. The comparison of beta-thymosin homologues among metazoa supports an arthropod-nematode clade. J Mol Evol 2000, 51:378-381.
    • (2000) J Mol Evol , vol.51 , pp. 378-381
    • Manuel, M.1    Kruse, M.2    Muller, W.E.3    Le Parco, Y.4
  • 13
    • 0037143719 scopus 로고    scopus 로고
    • A phylogenetic analysis of myosin heavy chain type II sequences corroborates that Acoela and Nemertodermatida are basal bilaterians
    • 10.1073/pnas.172390199, 123241, 12177440
    • Ruiz-Trillo I, Paps J, Loukota M, Ribera C, Jondelius U, Baguna J, Riutort M. A phylogenetic analysis of myosin heavy chain type II sequences corroborates that Acoela and Nemertodermatida are basal bilaterians. Proc Natl Acad Sci USA 2002, 99:11246-11251. 10.1073/pnas.172390199, 123241, 12177440.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 11246-11251
    • Ruiz-Trillo, I.1    Paps, J.2    Loukota, M.3    Ribera, C.4    Jondelius, U.5    Baguna, J.6    Riutort, M.7
  • 14
    • 0036184428 scopus 로고    scopus 로고
    • Testing the new animal phylogeny: first use of combined large-subunit and small-subunit rRNA gene sequences to classify the protostomes
    • 10.1093/oxfordjournals.molbev.a004082, 11861888
    • Mallatt J, Winchell CJ. Testing the new animal phylogeny: first use of combined large-subunit and small-subunit rRNA gene sequences to classify the protostomes. Mol Biol Evol 2002, 19:289-301. 10.1093/oxfordjournals.molbev.a004082, 11861888.
    • (2002) Mol Biol Evol , vol.19 , pp. 289-301
    • Mallatt, J.1    Winchell, C.J.2
  • 15
    • 0344952061 scopus 로고    scopus 로고
    • The evolutionary position of nematodes
    • 10.1186/1471-2148-2-7, 102755, 11985779
    • Blair JE, Ikeo K, Gojobori T, Hedges SB. The evolutionary position of nematodes. BMC Evol Biol 2002, 2:7. 10.1186/1471-2148-2-7, 102755, 11985779.
    • (2002) BMC Evol Biol , vol.2 , pp. 7
    • Blair, J.E.1    Ikeo, K.2    Gojobori, T.3    Hedges, S.B.4
  • 16
    • 0345874732 scopus 로고    scopus 로고
    • Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis
    • 314272, 14707168
    • Wolf YI, Rogozin IB, Koonin EV. Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. Genome Res 2004, 14:29-36. 314272, 14707168.
    • (2004) Genome Res , vol.14 , pp. 29-36
    • Wolf, Y.I.1    Rogozin, I.B.2    Koonin, E.V.3
  • 17
    • 35848952076 scopus 로고    scopus 로고
    • Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation
    • 10.1093/molbev/msm207, 17893400
    • Zheng J, Rogozin IB, Koonin EV, Przytycka TM. Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation. Mol Biol Evol 2007, 24:2583-2592. 10.1093/molbev/msm207, 17893400.
    • (2007) Mol Biol Evol , vol.24 , pp. 2583-2592
    • Zheng, J.1    Rogozin, I.B.2    Koonin, E.V.3    Przytycka, T.M.4
  • 18
    • 27844438226 scopus 로고    scopus 로고
    • Genome-scale evidence of the nematode-arthropod clade
    • 10.1186/gb-2005-6-5-r41, 1175953, 15892869
    • Dopazo H, Dopazo J. Genome-scale evidence of the nematode-arthropod clade. Genome Biol 2005, 6:R41. 10.1186/gb-2005-6-5-r41, 1175953, 15892869.
    • (2005) Genome Biol , vol.6
    • Dopazo, H.1    Dopazo, J.2
  • 19
    • 40549115956 scopus 로고    scopus 로고
    • Improvement of molecular phylogenetic inference and the phylogeny of Bilateria
    • Lartillot N, Philippe H. Improvement of molecular phylogenetic inference and the phylogeny of Bilateria. Philos Trans R Soc B 2008, 363:1463-1472.
    • (2008) Philos Trans R Soc B , vol.363 , pp. 1463-1472
    • Lartillot, N.1    Philippe, H.2
  • 20
    • 77958450862 scopus 로고    scopus 로고
    • Deep genomic-scale analyses of the metazoa reject Coelomata: evidence from single- and multigene families analyzed under a supertree and supermatrix paradigm
    • 10.1093/gbe/evq016, 2997542, 20624736
    • Holton TA, Pisani D. Deep genomic-scale analyses of the metazoa reject Coelomata: evidence from single- and multigene families analyzed under a supertree and supermatrix paradigm. Genome Biol Evol 2010, 2:310-324. 10.1093/gbe/evq016, 2997542, 20624736.
    • (2010) Genome Biol Evol , vol.2 , pp. 310-324
    • Holton, T.A.1    Pisani, D.2
  • 21
    • 3943059570 scopus 로고    scopus 로고
    • High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome
    • 10.1038/nature02697, 15295601
    • Denver DR, Morris K, Lynch M, Thomas WK. High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome. Nature 2004, 430:679-682. 10.1038/nature02697, 15295601.
    • (2004) Nature , vol.430 , pp. 679-682
    • Denver, D.R.1    Morris, K.2    Lynch, M.3    Thomas, W.K.4
  • 22
    • 0141609706 scopus 로고    scopus 로고
    • Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, γ-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models
    • 10.1016/S1055-7903(03)00115-5, 12878459
    • Waddell PJ, Shelley S. Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, γ-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models. Mol Phylogenet Evol 2003, 28:197-224. 10.1016/S1055-7903(03)00115-5, 12878459.
    • (2003) Mol Phylogenet Evol , vol.28 , pp. 197-224
    • Waddell, P.J.1    Shelley, S.2
  • 23
    • 74249106740 scopus 로고    scopus 로고
    • PhyloPattern: regular expression to identify complex patterns in phylogenetic trees
    • 10.1186/1471-2105-10-298, 2759962, 19765311
    • Gouret P, Thompson JD, Pontarotti P. PhyloPattern: regular expression to identify complex patterns in phylogenetic trees. BMC Bioinformatics 2009, 10:298. 10.1186/1471-2105-10-298, 2759962, 19765311.
    • (2009) BMC Bioinformatics , vol.10 , pp. 298
    • Gouret, P.1    Thompson, J.D.2    Pontarotti, P.3
  • 24
    • 0027759230 scopus 로고
    • So, what about the molecular clock hypothesis?
    • 10.1016/0959-437X(93)90011-D, 8118215
    • Li WH. So, what about the molecular clock hypothesis?. Curr Opin Genet Dev 1993, 3:896-901. 10.1016/0959-437X(93)90011-D, 8118215.
    • (1993) Curr Opin Genet Dev , vol.3 , pp. 896-901
    • Li, W.H.1
  • 25
    • 0031949306 scopus 로고    scopus 로고
    • Duplication-based measures of difference between gene and species trees
    • 10.1089/cmb.1998.5.135, 9541877
    • Eulenstein O, Mirkin B, Vingron M. Duplication-based measures of difference between gene and species trees. J Comput Biol 1998, 5:135-148. 10.1089/cmb.1998.5.135, 9541877.
    • (1998) J Comput Biol , vol.5 , pp. 135-148
    • Eulenstein, O.1    Mirkin, B.2    Vingron, M.3
  • 26
    • 84877152040 scopus 로고    scopus 로고
    • Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem
    • 10.1186/1471-2105-13-S10-S14, 3521216, 23282138
    • Górecki P, Eulenstein O. Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem. BMC Bioinformatics 2012, 13(Suppl 10):S14. 10.1186/1471-2105-13-S10-S14, 3521216, 23282138.
    • (2012) BMC Bioinformatics , vol.13 , Issue.SUPPL. 10
    • Górecki, P.1    Eulenstein, O.2
  • 27
    • 41149083635 scopus 로고    scopus 로고
    • Remote access to ACNUC nucleotide and protein sequence databases at PBIL
    • 10.1016/j.biochi.2007.07.003, 17825976
    • Gouy M, Delmotte S. Remote access to ACNUC nucleotide and protein sequence databases at PBIL. Biochimie 2008, 90:555-562. 10.1016/j.biochi.2007.07.003, 17825976.
    • (2008) Biochimie , vol.90 , pp. 555-562
    • Gouy, M.1    Delmotte, S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.