Table 1 - . Comparative analyses used to evaluate convergent and parallel evolution, with most used software and associated references.

Analysis		Softwares		References
Phylogenetic Tree Inference (Topo) Analysis of Evolutionary Rates (BL) Concordance factor of genes (gCFs) Concordance factor of sites (sCFs) Phylogenetic signal (PS)	Topo and BL	RaxML		Stamatakis, 2006
		IQTree		Nguyen et al., 2015; Minh et al., 2020b
		MrBayes		Ronquist & Huelsenbeck, 2003
		BEAST		Drummond & Rambaut, 2007; Bouckaert et al., 2014
	BL	aaML	PAML	Yang, 2007
	gCFs	IQTree		Minh et al., 2020a
	sCFs	IQTree		Mo et al., 2023
	PS	SH-test	CONSEL	Shimodaira and Hasegawa, 2001
Correlations between morphotypes and sequence rates		Forward Genomics		Hiller et al., 2012; Prudent et al., 2016
		TraitRateProp		Levy et al., 2017
		TraitRELAX		Halabi et al., 2020
		RERconverge		Kowalczyk et al., 2019
		Coevol		Lartillot & Poujol, 2011
		PhyloAcc		Hu et al., 2019
		PhyloAcc-GT		Yan et al., 2022
Ancestral state reconstruction		make.simmap/phytools	R	Revell, 2012
		baseML or codeML	PAML	Yang, 2007
Selection tests (Branch/Clade Model)		codeML	PAML	Yang, 2007
		aBSREL	HyPhy	Smith et al., 2015
		BUSTED		Murrell et al., 2015
		RELAX		Wertheim et al., 2015
Selection Tests (Branch-site Model)		codeML	PAML	Yang, 2007
		FEL	HyPhy	Pond et al., 2005
		FUBAR		Murrell et al., 2013
		MEME		Murrell et al., 2012
		SLAC		Pond et al., 2005