Abstract
The Perfect Phylogeny Problem is a classical problem in computational evolutionary biology, in which a set of species/taxa is described by a set of qualitative characters. In recent years, the problem has been shown to be NP-Complete in general, while the different fixed parameter versions can each be solved in polynomial time. In particular, Agarwala and Fernandez-Baca have developed an O(23r (nk3 + k4)) algorithm for the perfect phylogeny problem for n species defined by k r-state characters. Since commonly the character data is drawn from alignments of molecular sequences, k is the length of the sequences and can thus be very large (in the hundreds or thousands). Thus, it is imperative to develop algorithms which run efficiently for large values of k. In this paper we make additional observations about the structure of the problem and produce an algorithm for the problem that runs in time O(22rk2n). We also show how it is possible to efficiently build a structure that implicitly represents the set of all perfect phylogenies, and to randomly sample from that set.
| Original language | English (US) |
|---|---|
| Title of host publication | Proceedings of the 6th Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 1995 |
| Publisher | Association for Computing Machinery |
| Pages | 595-603 |
| Number of pages | 9 |
| ISBN (Electronic) | 0898713498 |
| State | Published - Jan 22 1995 |
| Externally published | Yes |
| Event | 6th Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 1995 - San Francisco, United States Duration: Jan 22 1995 → Jan 24 1995 |
Publication series
| Name | Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms |
|---|
Other
| Other | 6th Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 1995 |
|---|---|
| Country | United States |
| City | San Francisco |
| Period | 1/22/95 → 1/24/95 |
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ASJC Scopus subject areas
- Software
- Mathematics(all)
Cite this
A fast algorithm for the computation and enumeration of perfect phylogenies when the number of character states is fixed. / Kannan, Sampath; Warnow, Tandy.
Proceedings of the 6th Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 1995. Association for Computing Machinery, 1995. p. 595-603 (Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
}
TY - GEN
T1 - A fast algorithm for the computation and enumeration of perfect phylogenies when the number of character states is fixed
AU - Kannan, Sampath
AU - Warnow, Tandy
PY - 1995/1/22
Y1 - 1995/1/22
N2 - The Perfect Phylogeny Problem is a classical problem in computational evolutionary biology, in which a set of species/taxa is described by a set of qualitative characters. In recent years, the problem has been shown to be NP-Complete in general, while the different fixed parameter versions can each be solved in polynomial time. In particular, Agarwala and Fernandez-Baca have developed an O(23r (nk3 + k4)) algorithm for the perfect phylogeny problem for n species defined by k r-state characters. Since commonly the character data is drawn from alignments of molecular sequences, k is the length of the sequences and can thus be very large (in the hundreds or thousands). Thus, it is imperative to develop algorithms which run efficiently for large values of k. In this paper we make additional observations about the structure of the problem and produce an algorithm for the problem that runs in time O(22rk2n). We also show how it is possible to efficiently build a structure that implicitly represents the set of all perfect phylogenies, and to randomly sample from that set.
AB - The Perfect Phylogeny Problem is a classical problem in computational evolutionary biology, in which a set of species/taxa is described by a set of qualitative characters. In recent years, the problem has been shown to be NP-Complete in general, while the different fixed parameter versions can each be solved in polynomial time. In particular, Agarwala and Fernandez-Baca have developed an O(23r (nk3 + k4)) algorithm for the perfect phylogeny problem for n species defined by k r-state characters. Since commonly the character data is drawn from alignments of molecular sequences, k is the length of the sequences and can thus be very large (in the hundreds or thousands). Thus, it is imperative to develop algorithms which run efficiently for large values of k. In this paper we make additional observations about the structure of the problem and produce an algorithm for the problem that runs in time O(22rk2n). We also show how it is possible to efficiently build a structure that implicitly represents the set of all perfect phylogenies, and to randomly sample from that set.
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M3 - Conference contribution
AN - SCOPUS:85010171599
T3 - Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms
SP - 595
EP - 603
BT - Proceedings of the 6th Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 1995
PB - Association for Computing Machinery
ER -