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I'm currently writing a paper on the comparison of virulence genes for a group of bacteria. I got my data from publicly-available whole genome sequences in NCBI. Now, I want to create a phylogenetic tree for these species but since I'm working from home, I'm using my old laptop that makes it hard for me to process data. Can you recommend any software/ site/ tutorial/ paper that I can use to generate a phylogenetic tree easily? This is also the first time that I will create a phylogenetic tree and I'm not sure how to proceed without downloading and processing too much data that my current laptop can't handle.

Thank you!

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  • $\begingroup$ What file format(s) is your data? standard phylo tree format is i.e. Newick or New Hampshire format... So you can just go on google and search "freeware Newick tree display program" or something. $\endgroup$ – DeltaEnfieldWaid Nov 23 '20 at 5:00
  • $\begingroup$ My data is actually the WGS in NCBI for 55 bacterial strains. Is there a way to create a tree out of these without downloading and processing a large size of data? $\endgroup$ – rimuru Nov 23 '20 at 8:11
  • $\begingroup$ what about their tree viewer? genetics informatics forum is called BioStars. $\endgroup$ – DeltaEnfieldWaid Nov 23 '20 at 16:39
  • $\begingroup$ @aliential The OP wants to create a tree, not just to visualize a tree. Rimuru show us a few of your bacterias, everything is about the size and the alignement step. If it is your first time then use blast to extract a well-aligned 2000 nucleotides region, then use online tools such as trex.uqam.ca/index.php $\endgroup$ – reuns Nov 23 '20 at 17:53
  • $\begingroup$ Will you be comparing each one of the virulence genes to each other? If the WGS sequence is annotated for your gene you can take those sequences and use software like MEGA to create a phylogenetic tree. But you have good internet and your laptop does not have enough processing power (you haven't provided laptop specs) use an online tool like @reuns mentioned. $\endgroup$ – Roni Saiba Nov 29 '20 at 3:05

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