Table 2.

ASTRAL-III-beta vs ASTRAL-III. Columns are defined similar to Table 1.

Model	Contraction	FN	|X|	|Y|	Quartet	Running
condition					score	time
avian-0.5X-500bp	None	−0.003	−3%	−9%	−0.02%	−48%
avian-1X-250bp	None	−0.001	−3%	−9%	0.00%	−56%
avian-1X-500bp	None	−0.001	−2%	−6%	0.00%	−50%
avian-1X-1000bp	None	−0.001	−1%	−4%	0.00%	−58%
avian-1X-1500bp	None	0.001	−1%	−4%	0.00%	−57%
avian-2X-500bp	None	−0.002	−2%	−4%	0.00%	−65%
avian-0.5X-500bp	10%	−0.003	−3%	−29%	−0.01%	−69%
avian-1X-250bp	10%	−0.001	−50%	−40%	0.00%	−81%
avian-1X-500bp	10%	0.003	−18%	−62%	−0.01%	−62%
avian-1X-1000bp	10%	0.000	−5%	−8%	0.00%	−61%
avian-1X-1500bp	10%	0.003	0%	−1%	0.00%	−55%
avian-2X-500bp	10%	−0.002	−14%	−18%	0.00%	−62%

Negative numbers indicate ASTRAL-III-beta has a larger value (i.e., has higher error, larger search space, better quartet scores, and is slower)