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Installing and executing ProtTest3 on Ubuntu

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Prottest3 is a software which is used to select a best-fit amino acid replacement model for a set of protein sequences [1]. ProtTest3 finds a best-fit model on the basis of the smallest value of one of three criterions:¬†Akaike Information Criterion (AIC), Corrected Akaike Information Criterion, Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT) selected by the user. In this article, we will learn how to download and install the command-line version of ProtTest3 on Ubuntu. Continue reading “Installing and executing ProtTest3 on Ubuntu” »

How to calculate dN, dS, and dN/dS ratio on a set of genes using MEGA?

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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?” »

Most widely used tools for phylogenetic tree customization

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Most of the times, it is a very tedious job to convert file formats in bioinformatics, especially when we are dealing with phylogeny. Most of the available online servers mess your file and the output format is also not supported by the other programs. Additionally, it is quite difficult to perform other customizations on the phylogeny tree. Continue reading “Most widely used tools for phylogenetic tree customization” »

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