The worst case complexity of maximum parsimony

Amir Carmel; Noa Musa-Lempel; Dekel Tsur; Michal Ziv-Ukelson

doi:10.1007/978-3-319-07566-2_9

The worst case complexity of maximum parsimony

Amir Carmel, Noa Musa-Lempel, Dekel Tsur, Michal Ziv-Ukelson

Department of Computer Science

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

1 Scopus citations

Abstract

One of the core classical problems in computational biology is that of constructing the most parsimonious phylogenetic tree interpreting an input set of sequences from the genomes of evolutionarily related organisms. We re-examine the classical Maximum Parsimony (MP) optimization problem for the general (asymmetric) scoring matrix case, where rooted phylogenies are implied, and analyze theworst case bounds of three approaches to MP: The approach of Cavalli-Sforza and Edwards [5], the approach of Hendy and Penny [12], and a new agglomerative, "bottomup" approach we present in this paper. We show that the second and third approaches are faster than the first by a factor of and Θ(n), respectively.

Original language	English
Title of host publication	Combinatorial Pattern Matching - 25th Annual Symposium, CPM 2014, Proceedings
Publisher	Springer Verlag
Pages	79-88
Number of pages	10
ISBN (Print)	9783319075655
DOIs	https://doi.org/10.1007/978-3-319-07566-2_9
State	Published - 1 Jan 2014
Event	25th Annual Symposium on Combinatorial Pattern Matching, CPM 2014 - Moscow, Russian Federation Duration: 16 Jun 2014 → 18 Jun 2014

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	8486 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	25th Annual Symposium on Combinatorial Pattern Matching, CPM 2014
Country/Territory	Russian Federation
City	Moscow
Period	16/06/14 → 18/06/14

ASJC Scopus subject areas

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/978-3-319-07566-2_9

Cite this

Carmel, A., Musa-Lempel, N., Tsur, D., & Ziv-Ukelson, M. (2014). The worst case complexity of maximum parsimony. In Combinatorial Pattern Matching - 25th Annual Symposium, CPM 2014, Proceedings (pp. 79-88). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 8486 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-319-07566-2_9

@inproceedings{b584e026d345478585f5e6b1b797796a,

title = "The worst case complexity of maximum parsimony",

abstract = "One of the core classical problems in computational biology is that of constructing the most parsimonious phylogenetic tree interpreting an input set of sequences from the genomes of evolutionarily related organisms. We re-examine the classical Maximum Parsimony (MP) optimization problem for the general (asymmetric) scoring matrix case, where rooted phylogenies are implied, and analyze theworst case bounds of three approaches to MP: The approach of Cavalli-Sforza and Edwards [5], the approach of Hendy and Penny [12], and a new agglomerative, {"}bottomup{"} approach we present in this paper. We show that the second and third approaches are faster than the first by a factor of and Θ(n), respectively.",

author = "Amir Carmel and Noa Musa-Lempel and Dekel Tsur and Michal Ziv-Ukelson",

year = "2014",

month = jan,

day = "1",

doi = "10.1007/978-3-319-07566-2_9",

language = "English",

isbn = "9783319075655",

series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

publisher = "Springer Verlag",

pages = "79--88",

booktitle = "Combinatorial Pattern Matching - 25th Annual Symposium, CPM 2014, Proceedings",

address = "Germany",

note = "25th Annual Symposium on Combinatorial Pattern Matching, CPM 2014 ; Conference date: 16-06-2014 Through 18-06-2014",

}

Carmel, A, Musa-Lempel, N, Tsur, D & Ziv-Ukelson, M 2014, The worst case complexity of maximum parsimony. in Combinatorial Pattern Matching - 25th Annual Symposium, CPM 2014, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 8486 LNCS, Springer Verlag, pp. 79-88, 25th Annual Symposium on Combinatorial Pattern Matching, CPM 2014, Moscow, Russian Federation, 16/06/14. https://doi.org/10.1007/978-3-319-07566-2_9

The worst case complexity of maximum parsimony. / Carmel, Amir; Musa-Lempel, Noa; Tsur, Dekel et al.
Combinatorial Pattern Matching - 25th Annual Symposium, CPM 2014, Proceedings. Springer Verlag, 2014. p. 79-88 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 8486 LNCS).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - The worst case complexity of maximum parsimony

AU - Carmel, Amir

AU - Musa-Lempel, Noa

AU - Tsur, Dekel

AU - Ziv-Ukelson, Michal

PY - 2014/1/1

Y1 - 2014/1/1

N2 - One of the core classical problems in computational biology is that of constructing the most parsimonious phylogenetic tree interpreting an input set of sequences from the genomes of evolutionarily related organisms. We re-examine the classical Maximum Parsimony (MP) optimization problem for the general (asymmetric) scoring matrix case, where rooted phylogenies are implied, and analyze theworst case bounds of three approaches to MP: The approach of Cavalli-Sforza and Edwards [5], the approach of Hendy and Penny [12], and a new agglomerative, "bottomup" approach we present in this paper. We show that the second and third approaches are faster than the first by a factor of and Θ(n), respectively.

AB - One of the core classical problems in computational biology is that of constructing the most parsimonious phylogenetic tree interpreting an input set of sequences from the genomes of evolutionarily related organisms. We re-examine the classical Maximum Parsimony (MP) optimization problem for the general (asymmetric) scoring matrix case, where rooted phylogenies are implied, and analyze theworst case bounds of three approaches to MP: The approach of Cavalli-Sforza and Edwards [5], the approach of Hendy and Penny [12], and a new agglomerative, "bottomup" approach we present in this paper. We show that the second and third approaches are faster than the first by a factor of and Θ(n), respectively.

UR - http://www.scopus.com/inward/record.url?scp=84958527548&partnerID=8YFLogxK

U2 - 10.1007/978-3-319-07566-2_9

DO - 10.1007/978-3-319-07566-2_9

M3 - Conference contribution

AN - SCOPUS:84958527548

SN - 9783319075655

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 79

EP - 88

BT - Combinatorial Pattern Matching - 25th Annual Symposium, CPM 2014, Proceedings

PB - Springer Verlag

T2 - 25th Annual Symposium on Combinatorial Pattern Matching, CPM 2014

Y2 - 16 June 2014 through 18 June 2014

ER -

Carmel A, Musa-Lempel N, Tsur D , Ziv-Ukelson M. The worst case complexity of maximum parsimony. In Combinatorial Pattern Matching - 25th Annual Symposium, CPM 2014, Proceedings. Springer Verlag. 2014. p. 79-88. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-319-07566-2_9

The worst case complexity of maximum parsimony

Abstract

Publication series

Conference

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this