Preserving inversion phylogeny reconstruction

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 7534 LNBI, Issue , 2012, Pages 1-13

  Bernt, Matthias ^a   Chao, Kun Mao ^b   Kao, Jyun Wei ^b   Middendorf, Martin ^a   Tannier, Eric ^c  

^a UNIVERSITY OF LEIPZIG   (Germany)

^b NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^c UNIVERSITÉ LYON 1   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ANCESTRAL GENOMES; ARBITRARY NUMBER; BURKHOLDERIA; GENE ORDERS; LINEAR STRUCTURES; LINEAR-TIME ALGORITHMS; NP COMPLETE; PHYLOGENY RECONSTRUCTION; PROTEOBACTERIA;

BIOINFORMATICS; BIOLOGY; CLUSTERING ALGORITHMS;

GENES;

EID: 84866664268     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-33122-0_1     Document Type: Conference Paper

References (21)

1. Belda, E., Moya, A., Silva, F.J.: Genome rearrangement distances and gene order phylogeny in γ-proteobacteria. Mol. Biol. Evol. 22, 1456-1467 (2005)
2. Bérard, S., Bergeron, A., Chauve, C., Paul, C.: Perfect sorting by reversals is not always difficult. IEEE/ACM Trans. Comput. Biol. Bioinf. 4, 4-16 (2007)
3. Bérard, S., Chauve, C., Paul, C.: A more efficient algorithm for perfect sorting by reversals. Inform. Process. Lett. 106, 90-95 (2008)
4. Bergeron, A., Chauve, C., de Montgolfier, F., Raffinot, M.: Computing common intervals of k permutations, with applications to modular decomposition of graphs. SIAM J. Discrete Math. 22, 1022-1039 (2008)
5. Bernt, M.: Gene Order Rearrangement Methods for the Reconstruction of Phylogeny. PhD thesis, Universität Leipzig (2010)
6. Bernt, M., Merkle, D., Middendorf, M.: Solving the preserving reversal median problem. IEEE/ACM Trans. Comput. Biol. Bioinf. 5, 332-347 (2008)
7. Bernt, M., Merkle, D., Ramsch, K., Fritzsch, G., Perseke, M., Bernhard, D., Schlegel, M., Stadler, P.F., Middendorf, M.: CREx: inferring genomic rearrangements based on common intervals. Bioinformatics 23, 2957-2958 (2007)
8. Booth, K., Lueker, G.: Testing for the consecutive ones property, interval graphs and graph planarity using PQ-tree algorithms. J. Comput. Syst. Sci. 13, 335-339 (1976)
9. Bouvel, M., Chauve, C., Mishna, M., Rossin, D.: Average-Case Analysis of Perfect Sorting by Reversals. In: Kucherov, G., Ukkonen, E. (eds.) CPM 2009. LNCS, vol. 5577, pp. 314-325. Springer, Heidelberg (2009)
10. Day, W.H.E., Sankoff, D.: Computational complexity of inferring phylogenies by compatibility. Syst. Zool. 35, 224-229 (1986)
11. Dutheil, J., Gaillard, S., Bazin, E., Glemin, S., Ranwez, V., Galtier, N., Belkhir, K.: Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics. BMC Bioinformatics 7(1), 188 (2006)
12. Feijao, P., Meidanis, J.: SCJ: A breakpoint-like distance that simplifies several rearrangement problems. IEEE/ACM Trans. Comput. Biol. Bioinf. 8, 1318-1329 (2011)
13. Fertin, G., Labarre, A., Rusu, I., Tannier, E., Vialette, S.: Combinatorics of Genome Rearrangements. MIT Press (2009)
14. Figeac, M., Varré, J.-S.: Sorting by Reversals with Common Intervals. In: Jonassen, I., Kim, J. (eds.) WABI 2004. LNCS (LNBI), vol. 3240, pp. 26-37. Springer, Heidelberg (2004)
15. Fitch, W.: Toward defining the course of evolution: minimum change for a specified tree topology. Syst. Zool. 20, 406-416 (1971)
16. Foulds, L.R., Graham, R.L.: The Steiner problem in phylogeny is NP-complete. Adv. Appl. Math. 3, 43-49 (1982)
17. Hannenhalli, S., Pevzner, P.A.: Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. In: ACM Symposium on Theory of Computing, pp. 178-189 (1995)
18. Heber, S., Stoye, J.: Finding All Common Intervals of k Permutations. In: Amir, A., Landau, G.M. (eds.) CPM 2001. LNCS, vol. 2089, pp. 207-218. Springer, Heidelberg (2001)
19. Penel, S., Arigon, A.M., Dufayard, J.F., Sertier, A.S., Daubin, V., Duret, L., Gouy, M., Perrière, G.: Databases of homologous gene families for comparative genomics. BMC Bioinformatics 10, S3 (2009)
20. Sankoff, D.: Edit Distance for Genome Comparison Based on Non-Local Operations. In: Apostolico, A., Galil, Z., Manber, U., Crochemore, M. (eds.) CPM 1992. LNCS, vol. 644, pp. 121-135. Springer, Heidelberg (1992)
21. Tannier, E., Zheng, C., Sankoff, D.: Multichromosomal median and halving problems under different genomic distances. BMC Bioinformatics 10, 120 (2009)