Authors:
Rogério Güths
1
;
Guilherme P. Telles
2
;
Maria Emilia M. T. Walter
3
and
Nalvo Almeida
1
Affiliations:
1
Federal University of Mato Grosso do Sul, Brazil
;
2
University of Campinas, Brazil
;
3
University of Brasilia, Brazil
Keyword(s):
Phylogeny, Character State Phylogeny, Live Phylogeny, Parsimony, Algorithms.
Abstract:
In the character-based phylogeny reconstruction for n objects and m characters, the input is an nm-matrix
such that position i; j keeps the state of character j for the object i and the output is a binary rooted tree, where
the input objects are represented as leaves and each node v is labeled with a string of m symbols v1 : : :vm,
v j representing the state of character j, with minimal number of state changes along the edges of the tree,
considering all characters. This is called the Large Parsimony Problem. Live Phylogeny theory generalizes
the phylogeny theory by admitting living ancestors among the taxonomic objects. This theory suits cases
of fast-evolving species like virus, and phylogenies of non-biological objects like documents, images and
database records. In this paper we analyze problems related to most parsimonious tree using Live Phylogeny.
We introduce the Large Live Parsimony Problem (LLPP), prove that it is NP-complete and provide a branch
and bound solution. We als
o introduce and solve a simpler version, Small Live Parsimony Problem (SLPP),
which is used in the branch and bound.
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