Sequences were aligned by ClustalW [ 49] implemented in the Molecular Evolution and Genetics Analysis MEGAA) software package version 5 [ 50].
The expected values for replacements were calculated on the basis of the computer simulation of cyclin molecular evolution with the package INDELible 1.03 [ 66].
Molecular evolution approaches and the software package Phylogenetic Analyses by Maximum Likelihood (PAML) were utilized to investigate the signature of selection that has acted on the mammalian CC chemokine receptor (CCR) gene family.
Chromatin also plays an active role in gene regulation as well as a general role in genome packaging and therefore its molecular evolution may play an equally important role in gene regulatory evolution (Babbitt 2010; Babbitt et al. 2010).
The tree topologies of these individual gene loci or clades were then used as input files for PAML package (v4.4) [ 47] in molecular evolution estimation.
We tested for a significant association between parasitism and rate of molecular evolution using a Wilcoxon signed ranks test in the SPlus package v8.2.
Codeml in the PAML package was used to test different models of molecular evolution for each gene.
To produce distance matrices for ultrametric and additive trees, we use the ESTEEM package EvolSeq, an Excel workbook that simulates the molecular evolution of DNA sequences.
The generated Bayesian trees served as the basis for the implementation of the maximum likelihood methods of the PAML package of programs [ 41] aiming at detecting adaptive molecular evolution under specific models of codon substitution.
Molecular evolution of OryzaTPS1s was analyzed using the codeml program in the PAML 4.4 package [ 29].
