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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
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Algorithms for Molecular Biology

ISSN: 1748-7188