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Constructing and Employing Tree Alignment Graphs for Phylogenetic Synthesis

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Algorithms for Computational Biology (AlCoB 2015)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9199))

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Abstract

Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper provides a theoretical foundation for the use of TAGs in phylogenetics. We provide a formal definition of TAG that — unlike previous definition — does not depend on the order in which input trees are provided. In the consensus case, when all input trees have the same leaf labels, we describe algorithms for constructing majority-rule and strict consensus trees using the TAG. When the input trees do not have identical sets of leaf labels, we describe how to determine if the input trees are compatible and, if they are compatible, to construct a supertree that contains the input trees.

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Notes

  1. 1.

    S. A. Smith, J. W. Brown, and C. E. Hinchliff (Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor), personal communication.

References

  1. Baum, D., Smith, S.: Tree Thinking: An Introduction to Phylogenetic, 1st edn. Roberts and Company, Englewood (2012)

    Google Scholar 

  2. Goldman, N., Yang, Z.: Introduction. statistical and computational challenges in molecular phylogenetics and evolution. Philos. Trans. Royal Soc. B Biol. Sci. 363(1512), 3889–3892 (2008)

    Article  Google Scholar 

  3. McMahon, M., Deepak, A., Fernández-Baca, D., Boss, D., Sanderson, M.: STBase: one million species trees for comparative biology. PLoS One 10(2), e0117987 (2015)

    Article  Google Scholar 

  4. Faircloth, B.C., McCormack, J.E., Crawford, N.G., Harvey, M.G., Brumfield, R.T., Glenn, T.C.: Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst. Biol. 61(5), 716–726 (2012)

    Article  Google Scholar 

  5. Lemmon, A.R., Emme, S.A., Lemmon, E.M.: Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst. Biol. 61(5), 727–744 (2012)

    Article  Google Scholar 

  6. McCormack, J.E., Faircloth, B.C., Crawford, N.G., Gowaty, P.A., Brumfield, R.T., Glenn, T.C.: Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis. Genome Res. 22, 746–754 (2012)

    Article  Google Scholar 

  7. Smith, S.A., Brown, J.W., Hinchliff, C.E.: Analyzing and synthesizing phylogenies using tree alignment graphs. PLoS Comput. Biol. 9(9), e1003223 (2013)

    Article  MathSciNet  Google Scholar 

  8. Berry, V., Bininda-Emonds, O., Semple, C.: Amalgamating source trees with different taxonomic levels. Syst. Biol. 62(2), 231–249 (2013)

    Article  Google Scholar 

  9. Berry, V., Semple, C.: Fast computation of supertrees for compatible phylogenies with nested taxa. Syst. Biol. 55(2), 270–288 (2006)

    Article  Google Scholar 

  10. Daniel, P., Semple, C.: A class of general supertree methods for nested taxa. SIAM J. Discrete Methods 19, 463–480 (2005)

    Article  MathSciNet  MATH  Google Scholar 

  11. Smith, S.A., Cranston, K.A., Allman, J.F., Brown, J.W., Burleigh, G., Chaudhary, R., Coghill, L., Crandall, K.A., Deng, J., Drew, B., Gazis, R., Gude, K., Hibbett, D.S., Hinchliff, C., Katz, L.A., IV, H.D.L. , McTavish, E.J., Owen, C.L., Ree, R., Rees, J.A., Soltis, D.E., Williams, T.: Synthesis of phylogeny and taxonomy into a comprehensive tree of life. (Under review)

    Google Scholar 

  12. Aho, A.V., Sagiv, Y., Szymanski, T.G., Ullman, J.D.: Inferring a tree from lowest common ancestors with an application to the optimization of relational expressions. SIAM J. Comput. 10(3), 405–421 (1981)

    Article  MathSciNet  MATH  Google Scholar 

  13. Semple, C., Steel, M.: Phylogenetics. Oxford University Press, Oxford (2003)

    MATH  Google Scholar 

  14. Constantinescu, M., Sankoff, D.: An efficient algorithm for supertrees. J. Classif. 12, 101–112 (1995)

    Article  MATH  Google Scholar 

  15. Ng, M.P., Wormald, N.C.: Reconstruction of rooted trees from subtrees. Discrete Appl. Math. 69(1–2), 19–31 (1996)

    Article  MathSciNet  MATH  Google Scholar 

  16. Semple, C., Steel, M.A.: A supertree method for rooted trees. Discrete Appl. Math. 105, 147–158 (2000)

    Article  MathSciNet  MATH  Google Scholar 

  17. Page, R.D.M.: Modified Mincut Supertrees. In: Guigó, R., Gusfield, D. (eds.) WABI 2002. LNCS, vol. 2452, pp. 537–551. Springer, Heidelberg (2002)

    Chapter  Google Scholar 

  18. Diestel, R.: Graph Theory. Springer, Heidelberg (2000)

    MATH  Google Scholar 

  19. Cormen, T.H., Leiserson, C.E., Rivest, R.E.: Introduction to Algorithms. MIT Press, Cambridge (1996)

    MATH  Google Scholar 

  20. Amenta, N., Clarke, F., St. John, K.: A linear-time majority tree algorithm. In: Benson, G., Page, R.D.M. (eds.) WABI 2003. LNCS (LNBI), vol. 2812, pp. 216–227. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Biology, University of Florida, Gainesville, FL, 32611, USA

    Ruchi Chaudhary & J. Gordon Burleigh

  2. Department of Computer Science, Iowa State University, Ames, IA, 50011, USA

    David Fernández-Baca

Authors
  1. Ruchi Chaudhary
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  2. David Fernández-Baca
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  3. J. Gordon Burleigh
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Corresponding author

Correspondence to Ruchi Chaudhary .

Editor information

Editors and Affiliations

  1. Research Group on Mathematical Linguistics, Rovira i Virgili University, Tarragona, Spain

    Adrian-Horia Dediu

  2. Faculty of Science, National Autonomous University of Mexico - UNAM, Mexico City, Mexico

    Francisco Hernández-Quiroz

  3. Research Group on Mathematical Linguistics, Rovira i Virgili University, Tarragona, Spain

    Carlos Martín-Vide

  4. Institute for Research in Applied Mathematics and Systems – IIMAS, National Autonomous University of Mexico - UNAM, Mexico City, Mexico

    David A. Rosenblueth

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© 2015 Springer International Publishing Switzerland

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Chaudhary, R., Fernández-Baca, D., Burleigh, J.G. (2015). Constructing and Employing Tree Alignment Graphs for Phylogenetic Synthesis. In: Dediu, AH., Hernández-Quiroz, F., Martín-Vide, C., Rosenblueth, D. (eds) Algorithms for Computational Biology. AlCoB 2015. Lecture Notes in Computer Science(), vol 9199. Springer, Cham. https://doi.org/10.1007/978-3-319-21233-3_8

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  • DOI: https://doi.org/10.1007/978-3-319-21233-3_8

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-21232-6

  • Online ISBN: 978-3-319-21233-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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