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I have used multiple sequences aligned file of protein data to generate a maximum parsimony tree, then I used the "bootstrap_trees(msa, times, tree_constructor)" function from biopython to generate bootstrap replicates of my MSA data.

I have my original tree and bootstrap replicates for my tree, I want to ask how do I compare the topology (using python/biopython) for my tree with the bootstrap replicates so that for each edge in original tree the bootstrap support is shown. (Bootstrap support is the number of bootstrap trees that edge appears in.)

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  • $\begingroup$ majority_consensus or similar? That said, MP is not a good method for protein trees. You should use a more sophisticated tree builder. $\endgroup$
    – user172818
    Commented Dec 25, 2018 at 3:48
  • $\begingroup$ Actually, I have tried the generating the bootstrap replicates for my msa data. Now I need to count the number of times the same branching pattern appears in the bootstap replicates. How can I do this? $\endgroup$
    – Sidra Younas
    Commented Dec 28, 2018 at 14:11
  • $\begingroup$ I understand the question, its doable in parsimony. RAxML has a default for doing this but you might need to change the output format. $\endgroup$
    – M__ ♦
    Commented Apr 20, 2020 at 17:31

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