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Multiple Sequence Alignment at the Terminal with Conda

Welcome back, everyone. Today I talk about how to perform multiple sequence alignment with 'muscle' and 'clustalw' within a terminal conda environment. We also pull sequences from NCBI using their 'datasets' package. The idea behind these aligners is to overlap the sequences as much as possible while minimizing the gaps which sometimes results in mismatch bases. Multiple sequence alignment is helpful for finding out how similar 2 potentially unknown sequences are, as well as finding out far diverged 2 orthologs are. Here we are downloading primate orthologs and viewing the similarity between them. The results match that 2 genes from the same species show HIGH similarity and thus closeness in a dendrogram. Let me know if you find this helpful. Please consider contributing to my Patreon where I may do merch, gather ideas for future content, and have further discussions:   / alexsoupir   ClustalW: https://anaconda.org/bioconda/clustalw http://wiki.christophchamp.com/index.... Muscle: https://anaconda.org/bioconda/muscle https://github.com/rcedgar/muscle NCBI Datasets: https://anaconda.org/conda-forge/ncbi... https://www.ncbi.nlm.nih.gov/datasets... To subset the fasta file to top-n sequences, see: https://ro-che.info/articles/2016-08-... Visualizations: https://www.ebi.ac.uk/Tools/msa/mview/ https://www.ncbi.nlm.nih.gov/projects... http://etetoolkit.org/treeview/