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

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

Tree	Description	nRF^a	LogL1^b	LogL2^c
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

^aETE 3 was used to estimate the average nRF (normalized RF) distance between the gene family tree and the species tree
^bThe maximum log likelihoods of gene trees were estimated on the basis of the MSA generated by our pipeline
^cThe maximum log likelihoods of gene trees were estimated on the basis of the MSA downloaded from Ensembl 83
*BEAST or StarBeast

ISSN: 1471-2105