Although the use of mixed models is possible in both maximum likelihood (ML, [ 98]) and Bayesian frameworks, the accuracy of the resulting tree, at least in a Bayesian framework, has recently been called into question [ 99], especially when reasonable levels of conflict exist between the different data partitions [ 100].
Clamping grids were also inspected for differences in model output under different data partitions.
Transfer of ribosomal components between divergent organisms: Screening individual ribosomal protein families for phylogenetic conflict, and assigning the sequences from the recipient and its descendants to different data partitions, will avoid averaging over transfers between less related organisms.
The sequence data for each protein were partitioned using MrBayes v.3.1.2 [ 65] and phylogenetic estimates were calculated from the different data partitions.
Because this ratio changes with each of the individual models built on different data partitions, AUC values may not be useful in accurately comparing relative model performance between or among our subspecies and regional models.
The technique treats the raw molecular data as a pairwise matrix of genetic distances between all possible combinations of P. marneffei isolates, with submatrices corresponding to the different hierarchical data partitions (here, the genetic differences between P. marneffei infecting different host individuals, host species, and geographic regions).
Incongruence between the data partitions representing different portions of the plastid genome was assessed via the incongruence length difference (ILD) test [ 110], implemented as the partition homogeneity test in PAUP*4.0d102 [ 111].
In comparison with Bayes factors between different partitioning strategies, partitioning by exon and intron outperformed all other partitioning schemes.
Before the phylogenetic analyses, the NT data was subjected to pairwise PHT [ 62] between data partitions of different loci under either un-weighted or six-parameter weighting parsimony scheme [ 63, 64] with PAUP* 4.0b10 [ 65], with heuristic search for 1000 replicates.
However, they only dealt with the different importance of data partitions within a frame, and they did not distinguish the importance between different video frame-types.
