Protein phylogeny reconstruction
I have 30 strain of bacteria. Each consists of approx 1,200 proteins. I wish to reconstruct A tree using orthologus set of proteins. Please suggest the steps.
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You should edit your question and add details on what you've tried so far.
A few minutes on google or reading some papers would serve you best.
It’s not clear what type of phylogeny you want, what your data is like etc, so we will be of limited help.
I have 30 strains of bacteria. Each strains consists of 1,200 proteins. I wish to identify those proteins sequences which are present in each strains. Then I want to reconstruct phylogenetic tree using those sequences.
You should use a tool like
roaryfor this then really: https://sanger-pathogens.github.io/Roary/