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  • Phylogeny using whole proteomes

    Dear all,

    I have the proteome (and genome) of several species of nematodes. I would like to build the phylogeny of these species. Ultimately I would like a newick tree (which I could use as an input for CAFE)

    Do you know how to build phylogenies from whole proteomes/genomes?

    Best,
    Sophie

  • #2
    It won't get you to a newick file or standard output format at present, and requires a shell script and a bit of work, but MASH is a fast and fascinating approach.

    You can use you genomes with it (not proteomes as far as I know), but read the cautionary note in the preprint too.

    Comment


    • #3
      Thanks for your answer! Mash seems like a very interesting tool indeed! I wonder if it wouldn't be possible to get a newick tree from it...
      I'll be studying it!

      Comment


      • #4
        Check out the "ape" package available in R.
        You can save the tree in newick format.

        Comment


        • #5
          Thank you for your answer!
          I actually was able to run Mash and then input the distance matrix into ape to build a phylogenetic tree (and get it in Newick format)! It worked very good and the analysis was done very fast.
          Ape is a very nice package. Thanks for pointing it out to me.

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