Table 1.

Softwares Used in Our Benchmark, with the Type of Method (ML, parsimony, or both), the Nature of the Input Trees (random tree, ML tree, tree with bootstrap-support values, or MCMC sample of trees), Whether the Method Is STA and Whether the Method Accounts for HGT.

Software	Method Type	Input Trees	STA	HGT	Ref.
RAxML-NG	ML	Random	No	No	Kozlov et al. (2019)
Notung	Parsimony	Supported ML	Yes	No	Chen et al. (2000)
Treerecs	Parsimony + ML	Supported ML	Yes	No	Comte et al. (2020)
Phyldog	ML	ML	Yes	No	Boussau et al. (2013)
EcceTERA	Parsimony	Supported ML or MCMC samples	Yes	Yes	Scornavacca et al. (2015)
ALE	ML	MCMC samples	Yes	Yes	Szöllősi, Rosikiewicz, et al. (2013)
GeneRax	ML	Random or ML	Yes	Yes	This paper