Table 4.

Data on the simulated datasets

	Tree 1	Tree 2	Tree 3	Pfam
Average sequence identity	19%	30%	42%	-
Alignment length	1080	629	597	404
Sequence length	173	177	169	171
Original number of sequences	32	33	46	-
Average number of sequences after MaxAlign	14.1	22.6	28.8	-
Average number of indels per sequence	66.6	54.3	48.5	32
Average length of indels	13.6	8.3	8.8	7

Description of the simulated alignments used for testing the accuracy of phylogenetic inference with MaxAlign and removal of gapped columns, as well as the Pfam estimates used to tune the simulation parameters.