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Table 1 ASTRAL-II versus ASTRAL-III. Average and standard error (inside parenthesis) are shown for changes in accuracy (normalized FN rate), quartet score, and search space size (|X|)

From: ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

Data set

Model condition

FN

|X|

Quartet score

avian

0.5X-500bp

−0.006 (0.007)

−3% (0)

−0.01% (0.01)

 

1X-1000bp

0.001 (0.002)

−1% (0)

0.00% (0.00)

 

1X-1500bp

0.004 (0.003)

−1% (0)

0.00% (0.00)

 

1X-250bp

0.004 (0.007)

−3% (0)

−0.01% (0.00)

 

1X-500bp

−0.001 (0.004)

−2% (0)

0.00% (0.00)

 

2X-500bp

−0.003 (0.003)

−2% (0)

0.00% (0.00)

S200

1000gt- 10−6

−0.001 (0.000)

0% (0)

0.00% (0.00)

 

200gt- 10−6

0.000 (0.001)

−5% (1)

0.00% (0.00)

 

50gt- 10−6

−0.001 (0.001)

−42% (2)

−0.06% (0.01)

 

1000gt- 10−7

0.001 (0.001)

−1% (0)

0.00% (0.00)

 

200gt- 10−7

−0.001 (0.001)

−6% (1)

0.00% (0.01)

 

50gt- 10−7

0.000 (0.002)

−47% (2)

−0.06% (0.01)

S100

1000gt-1600bp

0.000 (0.000)

−3% (0)

0.00% (0.00)

 

500gt-1600bp

0.000 (0.000)

−6% (1)

0.00% (0.00)

 

200gt-1600bp

0.000 (0.001)

−17% (1)

−0.01% (0.00)

 

50gt-1600bp

−0.001 (0.001)

−46% (3)

−0.01% (0.01)

 

1000gt-200bp

−0.001 (0.002)

−9% (1)

0.00% (0.00)

 

500gt-200bp

−0.001 (0.001)

−19% (1)

−0.01% (0.01)

 

200gt-200bp

−0.001 (0.001)

−40% (1)

−0.01% (0.00)

 

50gt-200bp

−0.002 (0.002)

−72% (1)

−0.05% (0.01)

 

1000gt-400bp

−0.001 (0.002)

−6% (1)

0.00% (0.00)

 

500gt-400bp

0.001 (0.001)

−12% (1)

−0.01% (0.00)

 

200gt-400bp

0.000 (0.001)

−29% (2)

−0.01% (0.01)

 

50gt-400bp

−0.005 (0.001)

−61% (2)

−0.02% (0.01)

 

1000gt-800bp

0.000 (0.000)

−4% (0)

0.00% (0.00)

 

500gt-800bp

0.001 (0.001)

−9% (1)

0.00% (0.00)

 

200gt-800bp

0.001 (0.000)

−22% (2)

−0.01% (0.01)

 

50gt-800bp

0.000 (0.001)

−52% (3)

−0.02% (0.01)

  1. FN: we show ASTRALIII−ASTRALII; negative numbers indicate ASTRALIII is more accurate. |X|: we show \(\frac {\text {ASTRALIII}-\text {ASTRALII}}{\text {ASTRALII}}\times 100\); negative numbers indicate that ASTRAL-III has a reduced search space. Quartet score: we show \(\frac {\text {ASTRALIII}-\text {ASTRALII}}{\text {ASTRALII}}\times 100\); positive numbers indicate that ASTRALIII has improved quartet scores. See Additional file 1: Figures S4–S7 for full distributions