Skip to main content
SpringerLink
Log in
Book cover

International Computing and Combinatorics Conference

COCOON 1997: Computing and Combinatorics pp 274–283Cite as

A matrix representation of phylogenetic trees

  • Session 8: Computational Biology II
  • Conference paper
  • First Online:

  • 170 Accesses

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 1276))

Abstract

In this paper we begin by describing two currently used methods for evaluating phylogenetic trees, one proposed by Fitch and Margoliash [5] and the other proposed by Saitou and Nei [7]. Both methods are heuristic in the sense that not all possible trees are tested to ensure that the best solution has been reached. We develop a matrix representation of unrooted binary trees. The problem of evaluating phylogenetic trees is then transformed into the standard linear least squares problem. Then we propose a matrix decomposition method for evaluating phylogenetic trees.

This work was partly supported by grants awarded by NSERC Canada.

This work was partly supported by grants awarded by the City University of Hong Kong and by the Chiang Ching-Kuo Foundation for Scholarly Studies.

Also at the University of California at Berkeley, CA, USA.

This is a preview of subscription content, log in via an institution.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Cavalli-Sforsza, L.L. and A.W.F. Edwards. 1967. Phylogenetic Analysis Models and Estimation Procedures. Evolution, 32, pp.550–570 (also published in Amer. J. Hum. Genet. 19, pp.233–257).

    Google Scholar 

  2. Cavalli-Sforsza, L.L. and W. S-Y. Wang. 1986. Spatial Distance and Lexical Replacement. Language, 62, pp.38–55.

    Google Scholar 

  3. Day, W.H.E. 1987. Computational-Complexity of Inferring Phylogenies from Dissimilarity Matrices. Bulletin of Mathematical Biology, 49, pp.46–467.

    Google Scholar 

  4. Felsenstein, J. An Alternating Least Squares Approach to Inferring Phylogenies from Pairwise Distances, Manuscript.

    Google Scholar 

  5. Fitch, W. and E. Margoliash. 1967. Construction of Phylogenetic Trees. Science, Vol. 155, No. 3760, pp.279–284.

    Google Scholar 

  6. Garey, M.R. and D.S. Johnson. 1979. Computers and Intractability: a Guide to the Theory of NP-Completeness, W.H. Freeman, New York.

    Google Scholar 

  7. Saitou, N. and M. Nei. 1987. The Neighbor-joining Method: A New Method for Reconstructing Phylogenetic Trees. Molecular Biology and Evolution, 4(4), pp.406–425.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Computer Science and Systems, McMaster University, L8S 4K1, Hamilton, Ontario, Canada

    Sanzheng Qiao

  2. Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong

    W. S-Y Wang

Authors
  1. Sanzheng Qiao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. W. S-Y Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Tao Jiang D. T. Lee

Rights and permissions

Reprints and permissions

Copyright information

© 1997 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Qiao, S., Wang, W.SY. (1997). A matrix representation of phylogenetic trees. In: Jiang, T., Lee, D.T. (eds) Computing and Combinatorics. COCOON 1997. Lecture Notes in Computer Science, vol 1276. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0045094

Download citation

  • DOI: https://doi.org/10.1007/BFb0045094

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-63357-0

  • Online ISBN: 978-3-540-69522-6

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation