Combining Combinatorial Algorithms and Sequence-Based Phylogeny Reconstruction Methods to Infer Meaningful Explicit Phylogenetic Networks – CoCoAlSeq

Reconstructing evolutionary histories of currently-living species is a crucial step towards
tackling major biological issues. Relationships among species are traditionally displayed in
tree-shaped diagrams called phylogenetic trees. However, such trees cannot represent reticulate
evolutionary events as recombination, hybridization and lateral gene transfer. Therefore,
phylogenetic networks were recently introduced to display evolutionary scenarios including such
events. Phylogenetic networks have been intensively studied from a mathematical and computer
science perspective. However, recent biological publications most often still use phylogenetic
trees even where a network would be more suitable, mainly because current methods do not yet
take the full biological complexity into account. In this project we aim at combining
combinatorial algorithms and sequence-based methods - generally much slower but potentially more
accurate - to reconstruct meaningful phylogenetic networks.