On building and comparing trees
Application to supertrees in phylogenetics
Résumé
The research work presented in this manuscript is of algorithmic kind: it is mainly composed of polynomial, fixed parameter and approximation algorithms, while hardness results are also mentioned.
This work is about building and comparing labelled trees. These objects find application in different areas, but notoriously in phylogenetics, where they represent evolutionary relationships of organisms or sequences.
Most of this work can be considered as investigating solutions to so-called \emph{supertree} problems. Supertrees are large trees built by a dynamic programming approach from smaller trees. For instance, the latter are gene trees from which a comprehensive tree on many living species is to be built, such as the \emph{Tree of Life}.
First definitions are introduced, then a part of the manuscript is dedicated to quartet tree building methods. The next part details tree comparison methods, mainly variants of the maximum agreement subtree method. Next follows a part on supertree problems in all generality.
The manuscript ends with a report of the research plan for the next few years.
Several journal papers illustrating the material described in this manuscript are adjoined in appendix.
This work is about building and comparing labelled trees. These objects find application in different areas, but notoriously in phylogenetics, where they represent evolutionary relationships of organisms or sequences.
Most of this work can be considered as investigating solutions to so-called \emph{supertree} problems. Supertrees are large trees built by a dynamic programming approach from smaller trees. For instance, the latter are gene trees from which a comprehensive tree on many living species is to be built, such as the \emph{Tree of Life}.
First definitions are introduced, then a part of the manuscript is dedicated to quartet tree building methods. The next part details tree comparison methods, mainly variants of the maximum agreement subtree method. Next follows a part on supertree problems in all generality.
The manuscript ends with a report of the research plan for the next few years.
Several journal papers illustrating the material described in this manuscript are adjoined in appendix.
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