Body: <p>I have used multiple sequences aligned file of protein data to generate a maximum parsimony tree, then I used the <code>"bootstrap_trees(msa, times, tree_constructor)"</code> function from biopython to generate bootstrap replicates of my MSA data.</p>
  
  <p>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.)</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-25T03:48:15.530Z
Comments.Text: [majority_consensus](http://biopython.org/DIST/docs/api/Bio.Phylo.Consensus-module.html#majority_consensus) or similar? That said, MP is not a good method for protein trees. You should use a more sophisticated tree builder.
Comments.UserDisplayName: user172818
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-28T14:11:31.973Z
Comments.Text: 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?
Comments.UserDisplayName: Sidra Younas
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-20T17:31:48.133Z
Comments.Text: I understand the question, its doable in parsimony. RAxML has a default for doing this but you might need to change the output format.
Comments.UserDisplayName: M__
Tags: <phylogenetics><python><phylogeny>
Title: How to get bootstrap support of phylogenetic tree?
ThreadText: # How to get bootstrap support of phylogenetic tree?
  
  (Asked by: username_0 on 2018-12-24)
  
  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.)
  
  **Tags:** phylogenetics, python, phylogeny
  
  > **Comments:**
  > **username_1**: [majority_consensus](http://biopython.org/DIST/docs/api/Bio.Phylo.Consensus-module.html#majority_consensus) or similar? That said, MP is not a good method for protein trees. You should use a more sophisticated tree builder.  
  > **username_0**: 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?  
  > **username_2**: I understand the question, its doable in parsimony. RAxML has a default for doing this but you might need to change the output format.  
  
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  ## 0 answers
  
  