Instead, the strains branched deeply within the Proteobacteria as shown in a phylogenetic tree created by maximum likelihood [19], Figure 3. Very similar tree topologies were found by neighbor-joining, maximum parsimony or minimum evolution methods using MEGA3 [20](data not shown).
The best tree obtained by maximum likelihood is presented in Figure 1 with bootstrap scores and posterior probabilities.
Additionally, a smaller phylogeny consisting of just human and opossum class I genes and the mouse Mill genes was also inferred by maximum likelihood (Additional file 1: Figure S3).
The phylogenetic relationship of the sequences obtained was investigated by comparing them to the database, followed by maximum likelihood tree construction (Table 1, Figures 2 and 3).
The phylogenetic tree in Figure 9, reconstructed by maximum likelihood and Bayesian analyses, indicates that similar gene arrangements reflect close phylogenetic affinity.
From these alignments, we estimated the number of nonsynonymous substitutions per nonsynonymous site (K a) for each of the three branches in figure 2 A by maximum likelihood, using our previously described software (Conant and Wagner 2003).
Fixing the phylogeny to the assumed relationships (see Figure 1), we estimated branch lengths by maximum likelihood, using the BASEML software from PAML v3.15 [ 70].
We reconstructed the phylogenetic trees by maximum likelihood method and neighbor-joining method with different models shown in figure 4 a, b, c).
Molecular Phylogenetic analysis by Maximum Likelihood method of IFIT proteins using MSA in Additional file 4 : Figure S2.
