IMADA - Department of Mathematics and Computer Science |
The order of the genes on the chromosomes of species can be used for inferring their phylogenetic relationship. The inference of the rearrangements that formed the gene orders of today's species and the ancestral arrangement of the genes are problems arising in this field. We present here new approaches for these problems. The CREx method (common interval rearrangement explorer) computes heuristically pairwise rearrangement scenarios for gene order data. CREx detects such events as patterns in the signed strong interval tree, a data structure representing gene groups that appear consecutively in a set of two gene orders. As phylogenetic events in such scenarios reversals, transpositions, reverse transpositions, and tandem duplication random loss (TDRL) operations are considered. This makes it well suited for studying the gene order of mitochondrial genomes.
Based on CREx a method called TreeREx (tree rearrangement explorer) is
proposed for solving the problem of finding a plausible and
parsimonious assignment of genomic rearrangement events to the edges
of a given phylogenetic tree. TreeREx tries to assign events to the
edges of the phylogenetic tree, such that the pairwise scenarios are
reflected on the paths of the tree. It is shown that TreeREx can
automatically infer the events and the ancestral gene orders for
realistic biological examples of mitochondrial gene orders.
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