Ancestral reconstruction by asymmetric Wagner parsimony over continuous characters and squared parsimony over distributions

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

Volumn 5267 LNBI, Issue , 2008, Pages 72-86

  Csurös, Miklós ^a  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMIC TECHNIQUES; ARCHAEA; DISTANCE MEASURE; FEATURE SPACE; FINITE DISTRIBUTION; GENE CONTENT; LINEAR TIME; PARSIMONY ANALYSIS; REGULATORY SEQUENCES;

LAWS AND LEGISLATION;

IMAGE SEGMENTATION;

EID: 70449574265     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-87989-3_6     Document Type: Conference Paper

References (22)

1. Felsenstein, J.: Inferring Phylogenies. Sinauer Associates, Sunderland (2004)
2. Farris, J.S.: Methods for computing Wagner trees. Syst. Zool. 19, 83-92 (1970)
3. Swofford, D.L., Maddison, W.P.: Reconstructing ancestral states using Wagner parsimony. Math. Biosci. 87, 199-229 (1987)
4. Maddison, W.P.: Squared-change parsimony reconstructions of ancestral states for continuous-valued characters on a phylogenetic tree. Syst. Zool. 40, 304-314 (1991)
5. Sankoff, D., Rousseau, P.: Locating the vertices of a Steiner tree in arbitrary metric space. Math. Program. 9, 240-246 (1975)
6. Hwang, F.K., Richards, D.S.: Steiner tree problems. Networks 22, 55-89 (1992)
7. Cunningham, C.W., Omland, K.E., Oakley, T.H.: Reconstructing ancestral character states: a critical reappraisal. Trends Ecol. Evol. 13, 361-366 (1998)
8. Pagel, M.: Inferring the historical patterns of biological evolution. Nature 401, 877-884 (1999)
9. Witmer, P.D., Doheny, K.F., Adams, M.K., Boehm, C.D., Dizon, J.S., Goldstein, J.L., Templeton, T.M., Wheaton, A.M., Dong, P.N., Pugh, E.W., Nussbaum, R.L., Hunter, K., Kelmenson, J.A., Rowe, L.B., Brownstein, M.J.: The development of a highly informative mouse simple sequence length polymorphism (SSLP) marker set and construction of a mouse family tree using parsimony analysis. Genome Res. 13, 485-491 (2003)
10. Caetano-Anollés, G.: Evolution of genome size in the grasses. Crop. Sci. 45, 1809-1816 (2005)
11. Omland, K.E.: Examining two standard assumptions of ancestral reconstructions: repeated loss of dichromatism in dabbling ducks (Anatini). Evolution 51, 1636-1646 (1997)
12. Koonin, E.V.: Comparative genomics, minimal gene sets and the last universal common ancestor. Nat. Rev. Microbiol. 1, 127-136 (2003)
13. Cormen, T.H., Leiserson, C.E., Rivest, R.L., Stein, C.: Introduction to Algorithms, 2nd edn. MIT Press, Cambridge (2001)
14. Rogers, J.S.: Deriving phylogenetic trees from allele frequencies. Syst. Zool., 52-63 (1984)
15. Schwartz, S., Silva, J., Burstein, D., Pupko, T., Eyras, E., Ast, G.: Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Res. 18, 88-103 (2008)
16. Irimia, M., Penny, D., Roy, S.W.: Coevolution of genomic intron number and splice sites. Trends Genet. 23, 321-325 (2007)
17. Csucombining double acute accentrös, M., Miklós, I.: A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer. In: Apostolico, A., Guerra, C., Istrail, S., Pevzner, P.A., Waterman, M. (eds.) RECOMB 2006. LNCS (LNBI), vol. 3909, pp. 206-220. Springer, Heidelberg (2006)
18. Iwasaki, W., Takagi, T.: Reconstruction of highly heterogeneous gene-content evolution across the three domains of life. Bioinformatics 23, i230-i239 (2007)
19. Makarova, K.S., Sorokin, A.V., Novichkov, P.S., Wolf, Y.I., Koonin, E.V.: Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. Biology Direct 2, 33 (2007)
20. Mirkin, B.G., Fenner, T.I., Galperin, M.Y., Koonin, E.V.: Algorithms for computing evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol. Biol. 3, 2 (2003)
21. Fukui, T., Atomi, H., Kanai, T., Matsumi, R., Fujiwara, S., Imanaka, T.: Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. Genome Res. 15, 352-363 (2005)
22. Brochier, C., Forterre, P., Gribaldo, S.: An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences. BMC Evol. Biol. 5, 36 (2005)