Tutorial on phylogenetics
In this step, you will learn how to reconstruct a phylogenetic tree of SARS-CoV-2 genomes.
The first step is generating a multiple sequence alignment using MAFFT. Then we will reconstruct a tree using IQtree webserver. Further, you will be visualising the phylogeny and the metadata provided on Microreact.org.
Sometimes when you align a large number of sequences using MAFFT it may introduce large sequences of gaps and a visual inspection is recommended. The alignment can be assessed using a genomic viewer like IGV or NCBI Multiple Sequence Alignment Viewer. Inaccurate gaps must be manually removed before the phylogenetic tree reconstruction.
If you would like to test this tutorial, there is a multi-FASTA file containing the SARS-CoV-2 genomes and the metadata file containing epidemiological data related to it available for download. In this tutorial, we have provided high-quality data and no gaps must be removed from the alignments, but you can still upload it on NCBI Multiple Sequence Alignment Viewer to inspect it.
Share with your colleagues if you have heard about these tools before. What metadata or genomic data do you think you could also add?
Making sense of genomic data: COVID-19 web-based bioinformatics
Making sense of genomic data: COVID-19 web-based bioinformatics
