Software

GenPhylo (by M. Cortada Garcia and A. Diéguez Moscardó): Generating heterogeneous data on gene trees as Python code; also as a Python package here
ASAQ (by M. Garrote): algebraic and semi-algebraic phylogenetic reconstruction for quartets

SAQ (by M. Garrote) semi-algebraic phylogenetic reconstruction for quartets
Erik+2 (by M. Casanellas and J.Fernández): software for quartet topology reconstruction via invariants.
SPIn (by A. Kezdierska) software for model selection of evolutionary models via invariants.
GenNon-h (by A. Kedzierska): software for generating sequences evolving under a (discrete-time) Markov process on a tree with given branch lengths.
EMPar (by A. Kedzierska) EM for parameter estimation of Markov models on trees