Table 1.

Summary of the methods used in the pipeline.

name	original method publication	level	executable or source available	median computing time on 2000 sites
identical	[20]	site	no, reimplemented (Python and C++)	55 s
topological	[1,27]	site	no, reimplemented (Python and C++)	5 s
TDG09	[19,25]	site	yes. Used a modified version. https://github.com/tamuri/tdg09	1648 s (27 min)
diffsel	[24]	site	yes: https://github.com/vlanore/diffsel	141084 s (39 h)
PCOC	[18]	site	yes: https://github.com/CarineRey/pcoc	181 s (3 min)
multinomial	—	site	no, implemented de novo (Python)	21 s
msd	[19]	gene	yes. Used a modified version. https://github.com/gilles-didier/Convergence	70 s