Hi,
I am trying to create a phylogenetic tree for sars-cov-2 on Rstudio. I'm not sure what type of data to download from the NCBI website. If you have created a phylogeny of any genus or family can please help me?
This is what I'm trying to have a phylogenetic tree of
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=694009&lvl=3&keep=1&srchmode=1&unlock
I would really appreciate a step by step guidance
Thanks you very much
If you have no prior experience in phylogenetic analysis, set aside R or any other platform/language, what compels you to do so in first place and even the hard way? Why not first learn the basics about the analysis and easier software?
@Taylor S.H
If you want to construct phylogenetic tree of SARS-CoV-2, follow easy instructions below;
1. Retrieve your target and perspective SARS-CoV-2 genome sequence from GISAID or NCBI database.
2. Do multiple sequence alignment of your sequence with retrieved sequences in "BioEdit" or any tool. BioEdit is the best option for alignment because it allows to edit, addition, deletion of sequences of target.
3. Use Mega 7/ Mega 10 and construct maximum likelyhood or neighbour joining phylogenetic tree.
Mega is offline tool, it allows editing, branching, coloring your tree.
I agree with the responses above. First, you need to get some experience in phylogeny reconstruction through easy-to-use tools, like MEGA. Basicaly, you need to recover a data set of homologous sequences. You need an algorithm to perform a multiple sequence alignment (MSA). Then you can use the MSA for phylogeny reconstruction. All these steps can be performed on R language using some packages and functions that implement phylogenetic methods on R or call external softwares that do so.
For manipulation of sequence data, you can use the package Biostrings.
For MSA, you can use ape and ips packages to call alignment softwares as external applications, like ClustalW, MUSCLE, MAFFT, etc.
For phylogeny reconstruction using parsimony, maximum-likelihood or Bayesian approaches, you can use functions from ape, ips, and phangorn packages.
For plotting and annotating phylogenetic trees, you can use ape, ggtree, treeio, phytools etc. packages.
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