Table 1. The 14 different MSA trimming strategies tested in this study.

Software	MSA trimming strategies	Approach	Parameter(s)	Reference
ClipKIT	ClipKIT: k	Keep parsimony-informative sites	kpi mode	This study
	ClipKIT: kg	Keep parsimony-informative sites and remove highly gappy sites	kpi-gappy mode; remove sites with 90% gaps
	ClipKIT: kc	Keep parsimony-informative and constant sites	kpic mode
	ClipKIT: kcg	Keep parsimony-informative and constant sites and remove highly gappy sites	kpic-gappy mode; remove sites with 90% gaps
	ClipKIT: g	Remove highly gappy sites	gappy mode; remove sites with 90% gaps
BMGE	BMGE 0.3	Remove sites with high entropy	Entropy threshold of 0.3	[3]
	BMGE		Default entropy threshold of 0.5
	BMGE 0.7		Entropy threshold of 0.7
Gblocks	Gblocks	Remove sites that are gap rich and highly variable	default	[1]
Noisy	Noisy	Predicts homoplastic sites and remove them	default	[15]
trimAl	trimAl: s	Remove highly gappy and variable sites	strict mode	[2]
	trimAl: sp	Remove highly gappy and variable sites	strictplus mode
	trimAl: go	Remove highly gappy sites	gappyout mode
No trimming	No trim	N/A	N/A	N/A

Each MSA trimming strategy tested by our study, the software used, a general description of its trimming approach, its parameters, and a citation for the software used are described here.

BMGE, Block Mapping and Gathering with Entropy; MSA, multiple sequence alignment; N/A, not applicable.