LG model (Le and Gascuel 2008) was selected, and a four-category GAMMA distribution was used.
Using the AIC scores, we selected the LG model (Le and Gascuel 2008) with α = 3.27 and P = 0.01.
The LG+I+G+F model (Le and Gascuel 2008) was recommended by ProtTest as the best model based on both AIC and BIC criteria.
Amino acid sequences of single-copy genes were extracted, aligned with MUSCLE, concatenated, and used for PhyML phylogenetic analyses with the LG model (Le and Gascuel 2008).
PhyML was run with the LG evolutionary model (Le and Gascuel 2008) and a gamma distribution with four categories of substitution rates (Γ4) and an estimated alpha parameter.
Model selection using ProtTest3 (Darriba et al. 2011) suggested that the alternative single matrix LG model (Le and Gascuel 2008) provided a better fit to the data under both the Akaike Information Criterion and the Bayesian Information Criterion than the JTT model.
The program returned the LG model (Le and Gascuel 2008) with a gamma model of rate heterogeneity, a proportion of invariable sites, and an empirical residue frequency as the best model.
Two maximum-likelihood analyses were performed, using the standard LG-I amino acid substitution model (Le and Gascuel 2008) and the Mollicutes-optimized MOLLI60 substitution model (Lemaitre et al. 2011), respectively.
This alignment was best-fit by the LG model (Le and Gascuel, 2008) with a gamma-distributed set of evolutionary rates (Yang and Kumar, 1996), according to the Akaike Information Criterion as implemented in PROTTEST (Abascal et al., 2005).
Maximum likelihood searches were carried out using Treefinder version October 2008 (Jobb et al. 2004) using the LG + I + Γ model (Le and Gascuel 2008), which was identified as the best fitting model of amino acid substitution with the "propose model" subroutine from Treefinder.
