Fixed topology alignment with recombination
In this paper, we study a new version of multiple sequence alignment, fixed topology alignment with recombination. We show that it cannot be approximated within any constant ratio unless P=NP. For a restricted version, we show that the problem is MAX-SNP-hard. This implies that there is no PTAS for...
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| Published in | Discrete Applied Mathematics Vol. 104; no. 1; pp. 281 - 300 |
|---|---|
| Main Authors | , , |
| Format | Journal Article |
| Language | English |
| Published |
Elsevier B.V
15.08.2000
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| Subjects | |
| Online Access | Get full text |
| ISSN | 0166-218X 1872-6771 |
| DOI | 10.1016/S0166-218X(00)00196-7 |
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| Abstract | In this paper, we study a new version of multiple sequence alignment,
fixed topology alignment with recombination. We show that it cannot be approximated within any constant ratio unless P=NP. For a restricted version, we show that the problem is MAX-SNP-hard. This implies that there is no PTAS for this version unless P=NP. We also propose approximation algorithms for a special case, where each internal node has at most one recombination child and any two
merge paths for different recombination nodes do not share any common node. |
|---|---|
| AbstractList | In this paper, we study a new version of multiple sequence alignment,
fixed topology alignment with recombination. We show that it cannot be approximated within any constant ratio unless P=NP. For a restricted version, we show that the problem is MAX-SNP-hard. This implies that there is no PTAS for this version unless P=NP. We also propose approximation algorithms for a special case, where each internal node has at most one recombination child and any two
merge paths for different recombination nodes do not share any common node. |
| Author | Li, Ming Ma, Bin Wang, Lusheng |
| Author_xml | – sequence: 1 givenname: Lusheng surname: Wang fullname: Wang, Lusheng email: lwang@cs.cityu.edu.hk organization: Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong – sequence: 2 givenname: Bin surname: Ma fullname: Ma, Bin organization: Department of Mathematics, Peking University, Beijing 100871, People's Republic of China – sequence: 3 givenname: Ming surname: Li fullname: Li, Ming email: mli@math.uwaterloo.ca organization: Department of Computer Science, University of Waterloo, Waterloo, ONT. N2L 3G1, Canada |
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| Keywords | Evolutionary tree Recombination Phylogeny Approximation algorithm Multiple sequence alignment Computational biology |
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Mol. Evol. doi: 10.1007/BF00182187 – ident: 10.1016/S0166-218X(00)00196-7_BIB9 doi: 10.1145/261342.571216 – ident: 10.1016/S0166-218X(00)00196-7_BIB21 |
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fixed topology alignment with recombination. We show that it cannot be approximated... |
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| SubjectTerms | Approximation algorithm Computational biology Evolutionary tree Multiple sequence alignment Phylogeny Recombination |
| Title | Fixed topology alignment with recombination |
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