Like the MONKEY method [ 12], PhyloScan uses the phylogenetic model of Neyman [ 38] and the efficient algorithm of Felsenstein [ 39] to evaluate the probability that a site in observed multiply-aligned sequence data is consistent with a transcription factor's motif model.
Using the phylogenetic mixture model gave a conditioned logdet tree that was more different from the 16S rRNA tree and the SHOT tree than when the data were not partitioned.
A conservation landscape (see Figure 2) was computed using the phylogenetic Hidden Markov Model phastcons [ 59].
Reconstruction of gene gain and loss during microsporidian evolution was performed using the phylogenetic gain loss-duplication model employed in the software packagain loss-duplication).
To perform parametric bootstraps, 1,000 Monte Carlo simulations of alignments of the same length than the complete cytochrome b were generated with SeqGen [ 46] using the phylogenetic trees and model parameters previously obtained.
From each alignment, we removed one species at a time and used the remaining sequences to reconstruct the homolog in the removed species (target species) with the maxAlike algorithm using the phylogenetic tree from the multiz phastCons model (see Supplementary Fig. S13).
This effect was most pronounced for PS that only retrieved an output when leaving the sequences unaligned and suppressing the use of the phylogenetic model.
> -wrap-foot> Figure 8 compares our without Φ ⃗ ROC SEMPPR-based estimates of S with those estimated using the FMutSel phylogenetic model of Yang and Nielsen (2008) using PAML (Yang 2007) for the 106 genes in the Rokas et al. (2003) data set.
Irrespective of the substitution model (GTR nt, JTT) used for the analysis, the phylogenetic model additionally involved four discrete categories of gamma distributed rates across sites (denoted + Γ4, [ 42]), plus an invariant site category (denoted + I).
The first piece of evidence is based on mathematical considerations of the theory behind the phylogenetic models used in the tests, while the final three are empirical.
