We have sequenced over 600 SARS-CoV-2 whole genomes of Bangladeshi Patients. Now for analyses need to make the phylogenetic tree. Before we did it using Nexstrain, this tool is not suitable as it does not filter the data properly now. I am not sure what is the reason. Can anybody give me a good suggestion on how I can make a Phylogenetic tree with over 1000 samples? Which are the good tools to do it?
Thanking you all in advance.
First do a MSA with MEGA-X or other suitable software. Galaxy platform is another great option as it is onile and dont require highly configured laptop. Then you can visualize the tree with Figtree or iTol. Thanks a lot
when I need to make tree with over thousands of samples how it be possible with MEGA-X? I am also using CLUSTAL OMEGA, which is also not suitable. I need some other database-type tools like Nexstarin.
Galaxy platform is suitable for you then. MEGA or Bioedit cant handle large amount of data
For Galaxy also need to upload all the files first. For data more than thousands from different parts of the world, it is not possible.
First, you could try to align your genomes using MAFTT and then revise it using BioEdit (both can handle big databases). Then again, you could try to re-run Nextstrain.