A phylogenetic definition of structure and further animations on the sequence space
Seminar Room 1, Newton Institute
We want to show pictures and animations illustrating possible novel ways to model sequence evolution, as well as discussing the importance of a definition of structure. Our phylogenetic definition of structure consists of three aspects: The substitution matrix, a neighbourhood system and the phylogenetic tree. The substitution matrix specifies the evolutionary dynamics of nucleotide evolution. However, the matrix is influenced by the neighbourhood system, that defines the interactions among sites in a DNA sequences. The phylogenetic tree introduces an additional dependency pattern in the observed sequences. To take all this aspects into account, we have developed SISSI (Simulating Site-Specific Interactions). SISSI simulates the evolution of a nucleotide sequence along a phylogenetic tree taking into account user defined site-specific interactions.Thus, it is possible to mimic sequence evolution under structural constraints. Based on illustrative examples and simulations, we will discuss the different definitions of structure, for example single minimum free energy and consensus structure, as well as our definition of structure from a phylogenetic point of view. This will be demonstrated with different phylogenetic animations.
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