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Volumn 2012, Issue 8, 2012, Pages 475-487

TreeCmp: Comparison of trees in polynomial time

Author keywords

Matching Cluster metric; Matching Split metric; Phylogenetics; Tree comparison; Tree metrics

Indexed keywords

ACCESS TO INFORMATION; ACCURACY; COMPARATIVE STUDY; COMPUTER INTERFACE; COMPUTER PROGRAM; INTERNET; MATHEMATICAL ANALYSIS; PHYLOGENETIC TREE; PHYLOGENETIC TREE CONSTRUCTION METHOD; REVIEW;

EID: 84864835922     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: 10.4137/EBO.S9657     Document Type: Review
Times cited : (91)

References (36)
  • 1
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2-Approximately Maximum-Likelihood trees for large alignments
    • Price MN, Dehal PS, Arkin AP. FastTree 2-Approximately Maximum-Likelihood trees for large alignments. PLoS One. 2010;5:e9490.
    • (2010) PLoS One. , vol.5
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 2
    • 65449148286 scopus 로고    scopus 로고
    • Using tree diversity to compare phylogenetic heuristics
    • Sul, S-J, Matthews S, Williams T. Using tree diversity to compare phylogenetic heuristics. BMC Bioinformatics. 2009;10(Suppl 4):S3.
    • (2009) BMC Bioinformatics. , vol.10 , Issue.SUPPL. 4
    • Sul, S.-J.1    Matthews, S.2    Williams, T.3
  • 4
  • 5
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • Robinson DF, Foulds LR. Comparison of phylogenetic trees. Math Biosci. 1981;53:131-47.
    • (1981) Math Biosci. , vol.53 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2
  • 6
    • 12044252586 scopus 로고
    • Distributions of tree comparison metrics-some new results
    • Steel MA, Penny D. Distributions of tree comparison metrics-some new results. Syst Biol. 1993;42:126-41.
    • (1993) Syst Biol. , vol.42 , pp. 126-141
    • Steel, M.A.1    Penny, D.2
  • 8
    • 0030311519 scopus 로고    scopus 로고
    • The Triples Distance for rooted bifurcating phylogenetic trees
    • Critchlow DE, Pearl DK, Qian C. The Triples Distance for rooted bifurcating phylogenetic trees. Syst Biol. 1996;45:323-34.
    • (1996) Syst Biol. , vol.45 , pp. 323-334
    • Critchlow, D.E.1    Pearl, D.K.2    Qian, C.3
  • 9
    • 84959752542 scopus 로고
    • Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units
    • Estabrook GF, McMorris FR, Meacham CA. Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units. Syst Biol. 1985;34:193-200.
    • (1985) Syst Biol. , vol.34 , pp. 193-200
    • Estabrook, G.F.1    McMorris, F.R.2    Meacham, C.A.3
  • 12
    • 0347512294 scopus 로고    scopus 로고
    • Subtree transfer operations and their induced metrics on evolutionary trees
    • Allen BL, Steel M. Subtree transfer operations and their induced metrics on evolutionary trees. Ann Comb. 2001;5:1-15.
    • (2001) Ann Comb. , vol.5 , pp. 1-15
    • Allen, B.L.1    Steel, M.2
  • 13
    • 0024748699 scopus 로고
    • Faster scaling algorithms for network problems
    • Gabow HN, Tarjan RE. Faster scaling algorithms for network problems. SIAM J Comp. 1989;18:1013-36.
    • (1989) SIAM J Comp. , vol.18 , pp. 1013-1036
    • Gabow, H.N.1    Tarjan, R.E.2
  • 14
    • 0343675970 scopus 로고
    • New scaling algorithms for the assignment and minimum mean cycle problems
    • Orlin JB, Ahuja RK. New scaling algorithms for the assignment and minimum mean cycle problems. Math Program. 1992;54:41-56.
    • (1992) Math Program. , vol.54 , pp. 41-56
    • Orlin, J.B.1    Ahuja, R.K.2
  • 15
    • 0023173192 scopus 로고
    • A shortest augmenting path algorithm for dense and sparse linear assignment problems
    • Jonker R, Volgenant A. A shortest augmenting path algorithm for dense and sparse linear assignment problems. Computing. 1987;38:325-40.
    • (1987) Computing. , vol.38 , pp. 325-340
    • Jonker, R.1    Volgenant, A.2
  • 16
    • 0347306743 scopus 로고    scopus 로고
    • Algorithms and codes for dense assignment problems: The state of the art
    • Dell'Amico M, Toth P. Algorithms and codes for dense assignment problems: the state of the art. Discrete Appl Math. 2000;100:17-48.
    • (2000) Discrete Appl Math. , vol.100 , pp. 17-48
    • Dell'Amico, M.1    Toth, P.2
  • 17
    • 0003002776 scopus 로고
    • Optimal algorithms for comparing trees with labeled leaves
    • Day WHE. Optimal algorithms for comparing trees with labeled leaves. J Classif. 1985;2:7-28.
    • (1985) J Classif. , vol.2 , pp. 7-28
    • Day, W.H.E.1
  • 18
    • 15244342170 scopus 로고    scopus 로고
    • Computing the Quartet Distance between evolutionary trees in time O(n log n)
    • Brodal GS, Fagerberg R, Pedersen CNS. Computing the Quartet Distance between evolutionary trees in time O(n log n), Algorithmica. 2003;38: 377-95.
    • (2003) Algorithmica , vol.38 , pp. 377-395
    • Brodal, G.S.1    Fagerberg, R.2    Pedersen, C.N.S.3
  • 19
    • 79957832529 scopus 로고    scopus 로고
    • A sub-cubic time algorithm for computing the quartet distance between two general trees
    • Nielsen J, Kristensen AK, Mailund T, Pedersen CNS. A sub-cubic time algorithm for computing the quartet distance between two general trees. Algorithms Mol Biol. 2011;6:15.
    • (2011) Algorithms Mol Biol. , vol.6 , pp. 15
    • Nielsen, J.1    Kristensen, A.K.2    Mailund, T.3    Pedersen, C.N.S.4
  • 21
  • 22
    • 0034100582 scopus 로고    scopus 로고
    • Distributions of cherries for two models of trees
    • McKenzie A, Steel M. Distributions of cherries for two models of trees. Math Biosci. 2000;164:81-92.
    • (2000) Math Biosci. , vol.164 , pp. 81-92
    • McKenzie, A.1    Steel, M.2
  • 23
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22:2688-90.
    • (2006) Bioinformatics. , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 25
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
    • Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59:307-21.
    • (2010) Syst Biol. , vol.59 , pp. 307-321
    • Guindon, S.1    Dufayard, J-F.2    Lefort, V.3    Anisimova, M.4    Hordijk, W.5    Gascuel, O.6
  • 26
    • 0030807655 scopus 로고    scopus 로고
    • BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data
    • Gascuel O. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol. 1997;14:685-95.
    • (1997) Mol Biol Evol. , vol.14 , pp. 685-695
    • Gascuel, O.1
  • 27
    • 0000122573 scopus 로고
    • PHYLIP-Phylogeny Inference Package (Version 3.2)
    • Felsenstein J. PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics. 1989;5:164-6.
    • (1989) Cladistics. , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 28
    • 0036943052 scopus 로고    scopus 로고
    • Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle
    • Desper R, Gascuel O. Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J Comput Biol. 2002;9: 687-705.
    • (2002) J Comput Biol. , vol.9 , pp. 687-705
    • Desper, R.1    Gascuel, O.2
  • 29
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406-25.
    • (1987) Mol Biol Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 30
    • 33744914841 scopus 로고    scopus 로고
    • Relaxed neighbor joining: A fast distancebased phylogenetic tree construction method
    • Evans J, Sheneman L, Foster J. Relaxed neighbor joining: a fast distancebased phylogenetic tree construction method. J Mol Evol. 2006;62:785-92.
    • (2006) J Mol Evol. , vol.62 , pp. 785-792
    • Evans, J.1    Sheneman, L.2    Foster, J.3
  • 31
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 1992;8:275-82.
    • (1992) Comput Appl Biosci. , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 32
    • 36549003111 scopus 로고    scopus 로고
    • A congruence index for testing topological similarity between trees
    • de Vienne DM, Giraud T, Martin OC. A congruence index for testing topological similarity between trees. Bioinformatics. 2007;23:3119-24.
    • (2007) Bioinformatics. , vol.23 , pp. 3119-3124
    • de Vienne, D.M.1    Giraud, T.2    Martin, O.C.3
  • 33
    • 14344251246 scopus 로고    scopus 로고
    • TreeJuxtaposer: Scalable tree comparison using FocusaContext with guaranteed visibility
    • Munzner T, Guimbretière F, Tasiran S, Zhang L, Zhou Y. TreeJuxtaposer: scalable tree comparison using FocusaContext with guaranteed visibility. ACM Trans Graph. 2003;22:453-62.
    • (2003) ACM Trans Graph. , vol.22 , pp. 453-462
    • Munzner, T.1    Guimbretière, F.2    Tasiran, S.3    Zhang, L.4    Zhou, Y.5
  • 34
    • 0034894278 scopus 로고    scopus 로고
    • PAL: An object-oriented programming library for molecular evolution and phylogenetics
    • Drummond A, Strimmer K. PAL: an object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics. 2001;17:662-3.
    • (2001) Bioinformatics. , vol.17 , pp. 662-663
    • Drummond, A.1    Strimmer, K.2
  • 35
    • 77950019666 scopus 로고
    • Review of the computer program Component
    • Slowinski JB. Review of the computer program Component. Cladistics. 1993;9:351-3.
    • (1993) Cladistics. , vol.9 , pp. 351-353
    • Slowinski, J.B.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.