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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Bibliographic Details
Published inDiscrete Applied Mathematics Vol. 104; no. 1; pp. 281 - 300
Main Authors Wang, Lusheng, Ma, Bin, Li, Ming
Format Journal Article
LanguageEnglish
Published Elsevier B.V 15.08.2000
Subjects
Approximation algorithm
Computational biology
Evolutionary tree
Multiple sequence alignment
Phylogeny
Recombination
Evolutionary tree
Recombination
Phylogeny
Approximation algorithm
Multiple sequence alignment
Computational biology
Online AccessGet full text
ISSN0166-218X
1872-6771
DOI10.1016/S0166-218X(00)00196-7

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Summary: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.
ISSN:0166-218X
1872-6771
DOI:10.1016/S0166-218X(00)00196-7