We introduce the first polynomial-time phylogenetic reconstruction algorithm under a model of sequence evolution allowing insertions and deletions—or indels. Given appropriate ...
In comparative genomics, various combinatorial models can be used to specify gene clusters — groups of genes that are co-located in a set of genomes. Several approaches have been...
Chaining fragments is a crucial step in genome alignment. Existing chaining algorithms compute a maximum weighted chain with no overlaps allowed between adjacent fragments. In prac...
We consider the following problem: given a forest of gene family trees on a set of genomes, find a first speciation which splits these genomes into two subsets and minimizes the ...