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Table 2 Detailed comparision of the differences between the ENCODE guide tree and the best maximum likelihood trees calculated from splid data derived from various alignment tools

From: Split-inducing indels in phylogenomic analysis

  ClustalW Dialign-TX Mafft Mafft G-INS-i Mafft L-INS-i Muscle Prank ProbConsRNA T-Coffee TBA/Multiz
Afrotheria × × × × × × × × ×
Sister group to Boreoeutheria Sister group to Boreoeutheria   Sister group to Boreoeutheria Sister group to Boreoeutheria Within Boreoeutheria Sister group to Xenarthra Sister group to (Laurasiatheria, Xenarthra) Sister group to (Laurasiatheria, Xenarthra) Sister group to Euarchontoglires
((elephant, rock hyrax), tenrec) × × × × × × × × ×
Xenarthra (Armadillo) Sister taxon to Epitheria Sister taxon to Epitheria Sister taxon to part of the paraphyletic Epitheria Sister taxon to Epitheria Sister taxon to Epitheria Sister taxon to Epitheria Sister taxon to Afrotheria Sister taxon to Laurasiatheria Sister taxon to Laurasiatheria Sister group to Epitheria
Boreoeutheria × × × × ×
 Laurasiatheria × × × × × × × × × ×
  Insectivora × × × × × × × × × ×
  Chiroptera × × × × × × × × × ×
  ((rfbat, flying fox), sbbat) × × × × × × × ×
  Carnivora × × × × × × × × × ×
  Horse (bats, horse) (Carn., horse) (Carn., horse) (Carn., horse) (cow, horse) ((bats, cow), horse) ((bats, cow), horse) (((bats, cow), Carn.), horse) (cow, horse) (Carn., horse)
  Cow ((bats, horse), cow) (((Carn., horse), bats), cow) (((Carn., horse), bats), cow) (bats, cow) (cow, horse) (bats, cow) (bats, cow) (bats, cow) (cow, horse) (((Carn., horse), bats), cow)
 Euarchontoglires × × × × × × × ×
  Glires × × × ×
   Rodentia × × × × ×
   Muroidea × × × × × × Basal within Epitheria × × × ×
   Rabbit Sister taxon to Muroidea Sister taxon to tree shrew; both sister group to Primata Basal within Euarchontoglires Sister taxon to tree shrew; both sister group to Rodentia Sister taxon to tree shrew; both sister group to Rodentia Sister taxon to Euarchontoglires Sister taxon to Rodentia Sister taxon to Rodentia Sister taxon to Primata Sister taxon to Rodentia
  Primata × × × × × × × × ×
   Strepsirrhini × × × × × × × × × ×
   Platyrrhini × × × × × × × × × ×
   (((squirrel monkey, marmoset), owl monkey), dusky titi) ×
   Catarrhini × × × × × × × × × ×
    Cercopithecidae × × × × × × × × × ×
    (((baboon, macaque), vervet), colobus) × × × × ×
    Hominoidea × × × × × × × × × ×
    (((chimp, human), orangutan), gibbon) × × × × × × ×
  Tree shrew In Glires; sister taxon to (Hystricomorpha, Sciuromorpha) Sister taxon to rabbit; both sister group to Primata Sister taxon to Rodentia Sister taxon to rabbit; both sister group to Rodentia Sister taxon to rabbit; both sister group to Rodentia Sister taxon to (Hystricomorpha, Sciuromorpha) Basal within Euarchontoglires Sister taxon to Strepsirrhini Sister taxon to remaining (Epitheria, Xenarthra) Sister taxon to Glires
\(d_{RF}\) 20 18 18 14 16 22 16 20 20 14
\(d'_{RF}\) 0.3030 0.2727 0.2727 0.2121 0.2424 0.3333 0.2424 0.3030 0.3030 0.2121
\(d_{Q}\) 2347 2980 2748 1892 2043 6376 4164 6951 9458 3932
\(d'_{Q}\) 0.0398 0.0506 0.0467 0.0321 0.0347 0.1082 0.0707 0.1180 0.1606 0.0668
  1. Splids (gap length \(\ge\) 2 bp) were extracted from the ENCODE regions containing sequence information for all taxa. For each tree the symmetric difference (Robinson–Foulds distance, \(d_{RF}\)), the normalized RF distance (\(d'_{RF}\)), the quartet distance (\(d_{Q}\), at most 58,905), and the normalized quartet distance (\(d'_{Q}\)) to the ENCODE guide tree is shown. rfbat = Rhinolophus ferrumequinum, sbbat = Myotis lucifugus, Carn. = Carnivora. “×” = monophyly/position recovered, “–” = monophyly/position not recovered. See text for details