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Volumn 7, Issue 1, 2012, Pages

Reconciling taxonomy and phylogenetic inference: Formalism and algorithms for describing discord and inferring taxonomic roots

Author keywords

Algorithms; Branch and bound; Convex coloring; Dynamic program; Phylogenetics; Taxononomy

Indexed keywords


EID: 84860334363     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-7-8     Document Type: Article
Times cited : (10)

References (14)
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    • Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool
    • 10.1186/1471-2105-8-402, 2228325, 17949484
    • Dalevi D, DeSantis T, Fredslund J, Andersen G, Markowitz V, Hugenholtz P. Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool. BMC Bioinformatics 2007, 8:402. 10.1186/1471-2105-8-402, 2228325, 17949484.
    • (2007) BMC Bioinformatics , vol.8 , pp. 402
    • Dalevi, D.1    DeSantis, T.2    Fredslund, J.3    Andersen, G.4    Markowitz, V.5    Hugenholtz, P.6
  • 2
    • 84857122937 scopus 로고    scopus 로고
    • An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
    • 10.1038/ismej.2011.139, 3280142, 22134646
    • McDonald D, Price M, Goodrich J, Nawrocki E, DeSantis T, Probst A, Andersen G, Knight R, Hugenholtz P. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. The ISME Journal 2012, 6:610-618. 10.1038/ismej.2011.139, 3280142, 22134646.
    • (2012) The ISME Journal , vol.6 , pp. 610-618
    • McDonald, D.1    Price, M.2    Goodrich, J.3    Nawrocki, E.4    DeSantis, T.5    Probst, A.6    Andersen, G.7    Knight, R.8    Hugenholtz, P.9
  • 4
    • 43649094696 scopus 로고    scopus 로고
    • Convex recolorings of strings and trees: Definitions, hardness results and algorithms
    • Moran S, Snir S. Convex recolorings of strings and trees: Definitions, hardness results and algorithms. Journal of Computer and System Sciences 2008, 74(5):850-869.
    • (2008) Journal of Computer and System Sciences , vol.74 , Issue.5 , pp. 850-869
    • Moran, S.1    Snir, S.2
  • 7
    • 79957799985 scopus 로고    scopus 로고
    • Improved bounds on Bell numbers and on moments of sums of random variables
    • Berend D, Tassa T. Improved bounds on Bell numbers and on moments of sums of random variables. Probability and Mathematical Statistics 2010, 30(2).
    • (2010) Probability and Mathematical Statistics , vol.30 , Issue.2
    • Berend, D.1    Tassa, T.2
  • 10
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • 10.1093/bioinformatics/btl446, 16928733
    • Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22(21):2688. 10.1093/bioinformatics/btl446, 16928733.
    • (2006) Bioinformatics , vol.22 , Issue.21 , pp. 2688
    • Stamatakis, A.1
  • 11
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2-approximately maximum-likelihood trees for large alignments
    • 10.1371/journal.pone.0009490, 2835736, 20224823
    • Price M, Dehal P, Arkin A. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 2010, 5(3):e9490. 10.1371/journal.pone.0009490, 2835736, 20224823.
    • (2010) PLoS One , vol.5 , Issue.3
    • Price, M.1    Dehal, P.2    Arkin, A.3
  • 12
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    • OCaml
    • OCaml. , http://caml.inria.fr/ocaml/index.en.html
  • 14
    • 14344261697 scopus 로고    scopus 로고
    • Rooting a phylogenetic tree with nonreversible substitution models
    • 10.1186/1471-2148-5-2, 544347, 15629063
    • Yap VB, Speed T. Rooting a phylogenetic tree with nonreversible substitution models. BMC Evolutionary Biology 2005, 5:2. 10.1186/1471-2148-5-2, 544347, 15629063.
    • (2005) BMC Evolutionary Biology , vol.5 , pp. 2
    • Yap, V.B.1    Speed, T.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.