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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. $\endgroup$
    – bandybabboon
    Nov 23, 2020 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, 2020 at 8:11
  • $\begingroup$ what about their tree viewer? genetics informatics forum is called BioStars. $\endgroup$
    – bandybabboon
    Nov 23, 2020 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, 2020 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, 2020 at 3:05

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