Skip to main content

Table 1 Gene tree maximum log likelihoods based on MSAs and nRF distance from the species tree

From: Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family

Tree Description nRFa LogL1b LogL2c
Tree 1 Sequence only 0.31 −28,470 −31,425
Tree 2 ALE following BEAST 0.12 −28,479 −31,456
Tree 3 *BEAST following ALE and BEAST 0.14 −28,462 −31,423
Tree 4 Ensembl 0.21 −28,585 −31,536
  1. aETE 3 was used to estimate the average nRF (normalized RF) distance between the gene family tree and the species tree
  2. bThe maximum log likelihoods of gene trees were estimated on the basis of the MSA generated by our pipeline
  3. cThe maximum log likelihoods of gene trees were estimated on the basis of the MSA downloaded from Ensembl 83
  4. *BEAST or StarBeast