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how to perform phylogeny to know the evolution of strains

Hi, I have 50 different strains, and each strains has 39 different protein sequences on them. Actually i want to see the distance between strains via phylogeny. How to do it please let me know, if anyone know anything. I knew its silly question but i really want to know how.

Thank you a lot!

raxml fasta
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written by Neel • Neel

2 answers

After you build a phylogenetic tree (see the tutorial of RAxML, for example. https://cme.h-its.org/exelixis/web/software/raxml/hands_on.html), you can make a distance matrix from the tree as described in Script To Calculate A Distance Matrix Based On Tree File

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written by shelkmike shelkmike

Thank you for you time!

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written by Neel • Neel

General steps of that procedure:

  • Make alignments of individual proteins
  • Trim the alignments
  • Concatenate the alignments
  • Infer a phylogenetic tree

I don't think anyone here has the capacity to explain the intricacies of all steps. Chances are you will need to research this on your own, or find someone to guide you in person.

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written by Mensur Dlakic Mensur Dlakic

THank you a lot, sir.

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written by Neel • Neel

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