how to perform phylogeny to know the evolution of strains

Question

[Neel]

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!

Answer 1

[shelkmike]

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

[Neel]

Thank you for you time!

Answer 2

[Mensur Dlakic]

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.

[Neel]

THank you a lot, sir.