If you want to get a quick idea about the non-synonymous vs synonymous (dN/dS) substitutions, you can easily use MEGA software . Although HYPHY/Datamonkey provides the best results regarding selection pressure analyses. MEGA also uses HYPHY program  to calculate the dN/dS substitutions rate. Here is how you can do it.
You will need a codon fasta file genes, if you have protein sequences, then convert them into nucleotide codon sequences.
open MEGA --> Align --> Edit/Build Alignment --> Retrieve sequences from a file. (If you already have an alignment file then skip this step).
Edit --> Select all --> Align by ClustalW/Muscle.
Save the session and export alignment in MEGA format (.meg).
Minimize the alignment window. Go to the main window and click on "Selection" --> "Estimate selection for each codon (Hyphy)".
It will prompt to select a .meg file, select it.
It will ask for analysis preferences as shown in Fig. 1. Choose according to your requirements and click "Compute".
Fig. 1 Analysis preference window for dN/dS substitution calculation using MEGA7.
Later, it will ask for the output format and output directory where you want to save the results. Click "Ok". Your job will be finished after a few minutes depending up on the number and length of sequences.
- Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular biology and evolution, 33(7), 1870-1874.
- Pond, S. L. K., & Muse, S. V. (2005). HyPhy: hypothesis testing using phylogenies. In Statistical methods in molecular evolution (pp. 125-181). Springer, New York, NY.
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