Sentence examples for between runs was checked from inspiring English sources
Once the average standard deviation of split frequencies was less than 0.01, as suggested by MrBayes 3.1.2 [ 82], convergence between runs was checked.
Three separate runs (with one cold and three hot chains) of five million generations each were undertaken and stationarity as well as convergence between the MCMC runs was checked using both Tracer v. 1.3 [49] and the online program AWTY [50].
Consistency of results across the five runs was checked visually.
Convergence of the two runs was checked in mutliple ways.
Datasets were run three times with a different starting seed, and consistency across runs was checked by eye.
Convergence of independent runs was checked with the software Tracer v1.4.
The runs were checked for quality and sufficient ESS (effective sample size) in Tracer 1.5.3.
Runs were checked for convergence and normal distribution in Tracer v1.5 [ 34].
10 and 5 × 10 generations for nucleotides and amino acids respectively were enough for reaching convergence between the runs, which was checked using Tracer v1.5 [ 37].
