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  An Improved Algorithm for the Macro-evolutionary Phylogeny Problem

Behzadi, B., & Vingron, M. (2006). An Improved Algorithm for the Macro-evolutionary Phylogeny Problem. In Combinatorial Pattern Matching (pp. 177-187). Berlin/Heidelberg: Springer.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-84E8-7 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-84E9-5
Genre: Book Chapter

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 Creators:
Behzadi, Behshad1, Author
Vingron, Martin2, Author              
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1Max Planck Society, ou_persistent13              
2Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              

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 Abstract: Macro-evolutionary processes (e.g., gene duplication and loss) have rarely been incorporated into gene phylogeny reconstruction methods. Durand et al. [5] have proposed a polynomial time dynamic programming algorithm to find the gene family tree that optimizes a macro-evolutionary criterion which is the weighted sum of the number of gene duplications and losses. The complexity of this algorithm is O(nm2) where n is the number of species and m is the maximum number of copies of the gene in a species. In this paper, we propose an improved algorithm with time complexity of O(nm) for solving this problem. We also show, that the problem can be solved in O(n) if unit costs are considered for both loss and duplication.

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Language(s): eng - English
 Dates: 2006-01-01
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: -
 Identifiers: eDoc: 309234
DOI: 10.1007/11780441
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Title: Combinatorial Pattern Matching
Source Genre: Book
 Creator(s):
Lewenstein, Moshe, Author
Valiente, Gabriel, Author
Affiliations:
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Publ. Info: Berlin/Heidelberg : Springer
Pages: 414 Volume / Issue: - Sequence Number: - Start / End Page: 177 - 187 Identifier: ISBN: 3-540-35455-7

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Title: Lecture Notes in Computer Science
Source Genre: Series
 Creator(s):
Goos, Gerhard, Editor
Hartmanis, Juris, Editor
van Leeuwen, and Jan, Editor
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Publ. Info: -
Pages: - Volume / Issue: 4009/2006 Sequence Number: - Start / End Page: - Identifier: -