The fine structure of galls in phylogenetic networks

INFORMS Journal on Computing

Volumn 16, Issue 4, 2004, Pages 459-469

  Gusfield, Dan ^a   Eddhu, Satish ^a   Langley, Charles ^b  

^a University of California   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Ancestral recombination graph; Bi convex graph; Molecular evolution; Phylogenetic networks; Recombination; SNP

Indexed keywords

ALGORITHMS; DATA ACQUISITION; GENETIC ENGINEERING; GRAPH THEORY; MUTAGENESIS; TREES (MATHEMATICS);

ANCESTRAL RECOMBINATION GRAPH; BI-CONVEX GRAPH; MOLECULAR EVOLUTION; PHYLOGENETIC NETWORKS; RECOMBINATION; SNP;

MOLECULAR BIOLOGY;

EID: 10044254311     PISSN: 10919856     EISSN: 15265528     Source Type: Journal    
DOI: 10.1287/ijoc.1040.0099     Document Type: Article

References (18)

1. Day, W. H., D. Sankoff. 1986. Computational complexity of inferring phylogenies by compatibility. Systematic Zoology 35 224-229.
2. Dragan, F. 2000. Strongly orderable graphs: A common generalization of strongly chordal and chordal bipartite graphs. Discrete Appl. Math. 99 427-442.
3. Felsenstein, J. 2004. Inferring Phylogenies. Sinauer, Sunderland, MA.
4. Gusfield, D. 1991. Efficient algorithms for inferring evolutionary history. Networks 21 19-28.
5. Gusfield, D. 1997. Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Cambridge University Press, Cambridge, UK.
6. Gusfield, D. 2004. Optimal, efficient reconstruction of root-unknown phylogenetic networks with constrained recombination. Technical report, Department of Computer Science, University of California, Davis, CA.
7. Gusfield, D., S. Eddhu, C. Langley. 2003. Efficient reconstruction of phylogenetic networks (of SNPs) with constrained recombination. Proc. Second CSB Bioinformatics Conf. IEEE Press, Los Alamitos, CA.
8. Gusfield, D., S. Eddhu, C. Langley. 2004. Optimal, efficient reconstruction of phylogenetic networks with constrained recombination. J. Bioinformatics Comput. Biol. 2 173-213.
9. Hein, J. 1990. Reconstructing evolution of sequences subject to recombination using parsimony. Math. Biosci. 98 185-200.
10. Hein, J. 1993. A heuristic method to reconstruct the history of sequences subject to recombination. J. Molecular Evolution 36 396-405.
11. Kececioglu, J. D., D. Gusfield. 1998. Reconstructing a history of recombinations from a set of sequences. Discrete Appl Math. 88 239-260.
12. Myers, S. R., R. C. Griffiths. 2003. Bounds on the minimum number of recombination events in a sample history. Genetics 163 375-394.
13. Norborg, M., S. Tavare. 2002. Linkage disequilibrium: What history has to tell us. Trends Genetics 18 83-90.
14. Posada, D., K. Crandall. 2001. Intraspecific gene genealogies: Trees grafting into networks. Trends Ecology Evolution 16 37-45.
15. Schierup, M. H., J. Hein. 2000. Consequences of recombination on traditional phylogenetic analysis. Genetics 156 879-891.
16. Semple, C., M. Steel. 2003. Phylogenetics. Oxford University Press, Oxford, UK.
17. Song, Y., J. Hein. 2003. Parsimonious reconstruction of sequence evolution and haplotype blocks: Finding the minimum number of recombination events. Proc. 2003 Workshop Algorithms Bioinformatics, Lecture Notes in Computer Science, No. 2812, Springer-Verlag, Berlin, Germany, 287-302.
18. Wang, L., K. Zhang, L. Zhang. 2001. Perfect phylogenetic networks with recombination. J. Comput. Biol. 8 69-78.