Comparison of phylogenetic trees defined on different but mutually overlapping sets of taxa: A review.

Phylogenetic trees represent the evolutionary relationships and ancestry of various species or groups of organisms. Comparing these trees by measuring the distance between them is essential for applications such as tree clustering and the Tree of Life project. Many distance metrics for phylogenetic trees focus on trees defined on the same set of taxa.

GPTree Cluster: phylogenetic tree cluster generator in the context of supertree inference.

Summary: For many years, evolutionary and molecular biologists have been working with phylogenetic supertrees, which are oriented acyclic graph structures. In the standard approaches, supertrees are obtained by concatenating a set of phylogenetic trees defined on different but overlapping sets of taxa (i.e.

Invariant transformers of Robinson and Foulds distance matrices for Convolutional Neural Network.

The evolutionary histories of genes are susceptible of differing greatly from each other which could be explained by evolutionary variations in horizontal gene transfers or biological recombinations. A phylogenetic tree would therefore represent the evolutionary history of each gene, which may present different patterns from the species tree that defines the main evolutionary patterns. In addition, phylogenetic trees of closely related species should be merged, thus minimizing the topological conflicts they present and obtaining consensus trees (in the case of homogeneous data) or supertrees (in the case of heterogeneous data).