Term	Meaning
Homologs	Having a relationship through descent from at least one common ancestor
Family resemblance	Having an evolutionary relationship through intermediate sequences and common descent
Clique	A subgraph in a network where every member of the subgraph is connected to all other members
STT	Strong tree thinking: A perspective that sees homology statements as valid when the homologs have evolved down the branches of a bifurcating phylogenetic tree
PNT	Phylogenetic network thinking: A perspective that sees homology statements as valid when the homologs have evolved through tree-like processes, but allowing for some homologous recombination, thereby making a phylogenetic network.
GT	Goods thinking: A perspective that sees homology relationships encompass illegitimate recombination, fusion, and fission of evolving entities in addition to vertical descent. Gene evolution is expected at times to be very complex and involve merging of evolving entities.
N-rooted fusion networks	A new kind of network that depicts rooted networks with at least one fusion node and at least two roots.
TRIBES	Homologs that have a 1:1 correspondence in terms of being homologous for most or all their length.
TribeMCL	One of the most successful approaches to finding communities in networks of gene similarity.