Seminars in December 2011

  • Ilkyoo Choi (최일규), Avoiding Large Squares in Partial Words

    Avoiding Large Squares in Partial Words
    Ilkyoo Choi (최일규)
    Department of Mathematics, University of Illinois at Urbana-Champaign, IL, USA
    2011/12/22 Thu 4PM-5PM
    Given a fixed alphabet, a word of length n is an n-tuple with entries in the alphabet. A hole is a character outside the alphabet that is viewed as representing any letter of the alphabet. A partial word is a string where each character is a hole or belongs to the alphabet. Two partial words having the same length are compatible if they agree at each position where neither has a hole.
    A square is a word formed by concatenating two copies of a single word (no holes). A partial word W contains a square S if S is compatible with some (consecutive) subword of W. Let g(h,s) denote the maximum length of a binary partial word with h holes that contains at most s distinct squares. We prove that g(h,s)=∞ when s≥4 and when s=3 with h∈{0,1,2}; otherwise, g(h,s) is finite. Furthermore, we extend our research to cube-free binary partial words.
    This is joint work with Dr. Francine Blanchet-Sadri and Robert Mercas.
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  • Stefan Gruenewald, Quartets in Weakly Compatible Split Systems

    Quartets in Weakly Compatible Split Systems
    Stefan Gruenewald
    CAS-MPG Partner Institute for Computational Biology, Shanghai, China
    2011/12/9 Fri 4PM-5PM (Room 3433)
    A phylogenetic (i.e evolutionary) tree can be interpreted as a compatible split system, that is a collection of bipartitions of a finite set X such that, for all four elements of X, there are no two bipartitions in the collection that induce different splits of those four elements into two pairs. Such a split of a 4-set into two 2-sets is called a quartet, and a split system is said to display a quartet, if there is at least one split in the system that induces this quartet. In phylogenetics, it is often useful to allow more general than compatible split systems, in order to display contradicting signals in the data or to find evidence for reticulate evolution. One natural such generalization are weakly compatible split systems, where for every 4-set at most two of the three possible quartets are allowed to be displayed. The split decomposition algorithm (implemented in the Splitstree software) is a successful tool to construct weakly compatible split systems from distance data. However, weakly compatible split systems are not as well understood as compatible ones. For example, maximal compatible split systems, i.e. compatible split systems which become incompatible whenever a new split is added, correspond to binary trees and display one quartet for every 4-set. In contrast, maximal weakly compatible split systems often display less than the two quartets per 4-set that are allowed by definition. Indeed there are examples where no quartet is displayed for almost all 4-sets. This leaves the question what is the minimum cardinality of maximal weakly compatible split systems for given cardinality of X.
    In my talk I will introduce weakly compatible split systems and explain their relevance for phylogenetics, and I will present upper and lower bounds for the smallest number of quartets in maximal weakly compatible split systems.

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