Article

On the complexity of distance-based evolutionary tree reconstruction

Authors:

Yunhong ZhouAuthors Info & Claims

SODA '03: Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms

Pages 444 - 453

Published: 12 January 2003 Publication History

Abstract

We give the first tight lower bounds on the complexity of reconstructing k-ary evolutionary trees from additive distance data. We also consider the problem under DNA-based distance estimation assumptions, where the accuracy of distance data depends on the length of the sequence and the distance. We give the first o(n²) algorithm to reconstruct trees in this context, and prove a trade-off between the length of the DNA sequences and the number of distance queries needed to reconstruct the tree. We introduce new computational models for understanding this problem, which simplify the development of algorithms. We prove lower bounds in these models which apply to the type of techniques currently in use.

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Cited By

Kannan SMathieu CZhou H(2018)Graph Reconstruction and VerificationACM Transactions on Algorithms10.1145/319960614:4(1-30)Online publication date: 9-Aug-2018
https://dl.acm.org/doi/10.1145/3199606
Daskalakis CRoch S(2016)Species trees from gene trees despite a high rate of lateral genetic transferProceedings of the twenty-seventh annual ACM-SIAM symposium on Discrete algorithms10.5555/2884435.2884545(1621-1630)Online publication date: 10-Jan-2016
https://dl.acm.org/doi/10.5555/2884435.2884545
Micali SZhu Z(2016)Reconstructing Markov processes from independent and anonymous experimentsDiscrete Applied Mathematics10.1016/j.dam.2015.06.035200:C(108-122)Online publication date: 19-Feb-2016
https://dl.acm.org/doi/10.1016/j.dam.2015.06.035
Show More Cited By

Index Terms

On the complexity of distance-based evolutionary tree reconstruction
1. Applied computing
  1. Life and medical sciences
2. Mathematics of computing
  1. Discrete mathematics
    1. Graph theory
      1. Trees
  2. Mathematical analysis
    1. Numerical analysis
      1. Interpolation

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Published In

cover image ACM Conferences

SODA '03: Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms

January 2003

891 pages

ISBN:0898715385

Sponsors

SIAM Activity Group on Discrete Mathematics
SIGACT: ACM Special Interest Group on Algorithms and Computation Theory

Publisher

Society for Industrial and Applied Mathematics

United States

Publication History

Published: 12 January 2003

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Overall Acceptance Rate 411 of 1,322 submissions, 31%

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Cited By

Kannan SMathieu CZhou H(2018)Graph Reconstruction and VerificationACM Transactions on Algorithms10.1145/319960614:4(1-30)Online publication date: 9-Aug-2018
https://dl.acm.org/doi/10.1145/3199606
Daskalakis CRoch S(2016)Species trees from gene trees despite a high rate of lateral genetic transferProceedings of the twenty-seventh annual ACM-SIAM symposium on Discrete algorithms10.5555/2884435.2884545(1621-1630)Online publication date: 10-Jan-2016
https://dl.acm.org/doi/10.5555/2884435.2884545
Micali SZhu Z(2016)Reconstructing Markov processes from independent and anonymous experimentsDiscrete Applied Mathematics10.1016/j.dam.2015.06.035200:C(108-122)Online publication date: 19-Feb-2016
https://dl.acm.org/doi/10.1016/j.dam.2015.06.035
Chellappan VKrithivasan K(2014)Tree topology inference from leaf-to-leaf path lengths using Prüfer sequenceInternational Journal of Communication Networks and Distributed Systems10.1504/IJCNDS.2014.05943912:2(225-237)Online publication date: 1-Feb-2014
https://dl.acm.org/doi/10.1504/IJCNDS.2014.059439
Brown DTruszkowski J(2012)Fast phylogenetic tree reconstruction using locality-sensitive hashingProceedings of the 12th international conference on Algorithms in Bioinformatics10.1007/978-3-642-33122-0_2(14-29)Online publication date: 10-Sep-2012
https://dl.acm.org/doi/10.1007/978-3-642-33122-0_2
Brown DTruszkowski J(2011)Towards a practical O(n log n) phylogeny algorithmProceedings of the 11th international conference on Algorithms in bioinformatics10.5555/2039945.2039947(14-25)Online publication date: 5-Sep-2011
https://dl.acm.org/doi/10.5555/2039945.2039947
Brown DTruszkowski J(2011)Fast error-tolerant quartet phylogeny algorithmsProceedings of the 22nd annual conference on Combinatorial pattern matching10.5555/2018243.2018259(147-161)Online publication date: 27-Jun-2011
https://dl.acm.org/doi/10.5555/2018243.2018259
Bhamidi SRajagopal RRoch S(2010)Network delay inference from additive metricsRandom Structures & Algorithms10.5555/1841364.184136537:2(176-203)Online publication date: 1-Sep-2010
https://dl.acm.org/doi/10.5555/1841364.1841365
Gronau IMoran SSnir STeng S(2008)Fast and reliable reconstruction of phylogenetic trees with very short edgesProceedings of the nineteenth annual ACM-SIAM symposium on Discrete algorithms10.5555/1347082.1347124(379-388)Online publication date: 20-Jan-2008
https://dl.acm.org/doi/10.5555/1347082.1347124

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