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Table 3 Results for the large ENCODE data set. Splids \(\ge\) 2 bp were coded and trees were calculated with RAxML using the Gamma model for binary data and ascertainment bias correction

From: Split-inducing indels in phylogenomic analysis

 

Mafft G-INS-i

T-Coffee

TBA/Multiz

Number of sites

36,132,992

36,450,667

37,689,662

Number of splids

545,790

922,277

919,908

\(d_{RF}\)

16

16

12

\(d'_{RF}\)

0.2424

0.2424

0.1818

\(d_{Q}\)

5000

7494

3710

\(d'_{Q}\)

0.0849

0.1272

0.0630