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” »
Roary is a pangenome genome pipeline, which calculates pangenome of a set of related prokaryotic isolates [1]. It takes annotated assemblies in the gff3 format generated by Prokka [2] and provides the pangenome. The working methodology has been explained in our previous article. In this article, we will learn how to create the pangenome of a few isolated genome sequences using Roary [1] and Prokka [2]. Continue reading “How to create a pangenome of isolated genome sequences using Roary and Prokka?” »