Phylogenetic Networks
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of reticulate
evolution events, like hybridization between lineages, lateral gene transfer, recombination between genes, and
homoplasy. The first lecture will be devoted to phylogenetic trees, and it will lay down a foundation for the
study of phylogenetic networks, covering the inference of phylogenetic trees from (cladistic) character data
and (sequence alignment) distance data, the perfect phylogeny problem, the comparison of phylogenetic trees
by means of bipartitions, and the alignment of phylogenetic trees. In the second lecture, the problem of
inferring phylogenetic networks from (cladistic) character data and (sequence alignment) distance data will be
addressed in detail. The third lecture will be devoted to the problem of comparing phylogenetic networks by
means of tripartitions, and aligning the inferred phylogenetic networks.
T. Asano, P. Evans, R. Uehara, and G. Valiente. (2006). Site consistency in phylogenetic networks with recombination. In: Algorithms in Bioinformatics , volume 6 of Texts in Algorithmics, chapter 2, 15-26. College Publications.
D. Gusfield, S. Eddhu, and C. Langley. (2004). Optimal, efficient reconstruction of phylogenetic networks with constrained recombination. J. Bioinform. Comput . Biol., 2 (1):173-213.
G. Jin, L. Nakhleh, S. Snir, and T. Tuller. (2006). Maximum likelihood of phylogenetic networks. Bioinformatics , 22 (21):2604-2611.
A. Lozano, R. Pinter, O. Rokhlenko, G. Valiente, and M. Ziv-Ukelson. Seeded tree alignment and planar tanglegram layout. (2007). In: Proc. 7th Workshop on Algorithms in Bioinformatics , volume 4645 of Lecture Notes in Bioinformatics, 98-110.
B. M. E. Moret, L. Nakhleh, T. Warnow, C. R. Linder, A. Tholse, A. Padolina, J. Sun, and R. Timme. (2004). Phylogenetic networks: Modelling, reconstructibility, and accuracy. IEEE T. Comput. Biol. , 1 (1):13-23.
L. Nakhleh, T. Warnow, C. R. Linder, and K. S. John. (2005). Reconstructing reticulate evolution in species: Theory and practice. J. Comput. Biol ., 12 (6):796-811.
R. D. M. Page and G. Valiente. (2005). An edit script for taxonomic classifications. BMC Bioinformatics , 6 :208.