Processes of molecular innovation require tinkering and shifting in the function of existing genes.
Phylogeny.fr, created in 2008, has been designed to facilitate the execution of phylogenetic workflows, and is nowadays widely used.
The transfer distance (TD) was introduced in the classification framework and studied in the context of phylogenetic tree matching.
Nature. 2018 Apr;556(7702):452-456. doi: 10.1038/s41586-018-0043-0. Epub 2018 Apr 18.