If you want to get a quick idea about the non-synonymous vs synonymous (dN/dS) substitutions, you can easily use MEGA software [1]. Although HYPHY/Datamonkey provides the best results regarding selection pressure analyses. MEGA also uses HYPHY program [2] to calculate the dN/dS substitutions rate. Here is how you can do it. Continue reading “How to calculate dN, dS, and dN/dS ratio on a set of genes using MEGA?” »
In the last article on Bioinformatics Review, the utilization of Roary [1] and Prokka [2] was explained to create a pangenome from isolated genome sequences. This article is about installing these both packages on Ubuntu. Continue reading “Installing Roary and Prokka on Ubuntu” »
Structure modeling of chemical compounds finds essential application in the field of cheminformatics. It is used to study the structural stability, metal-ion bonding, the presence of electrons, closed and open shell energies, the reactivity of complexes, molecular orbital analyzes, molecular mechanics, and so on. There is some software available for structural modeling of chemical compounds/complexes and the most widely used are Gaussian [1] and ORCA [2]. Continue reading “How to do molecular orbital analysis to find d-orbitals involved in bonding in an organometallic compound?” »