title: Biopython bootstrapping phylogenetic trees with custom distance matrix
body: <p>I am trying to create a bootstrapped phylogenetic tree but instead of using raw multiple sequence alignment data and a standard scoring system, I want to use my own custom distance matrix that I have created.  I have currently looked at <a href="http://biopython.org/wiki/Phylo" rel="nofollow">http://biopython.org/wiki/Phylo</a> and have been able to create a single tree using my own custom distance matrix using the following code:</p>
  
  <pre><code>dm = TreeConstruction._DistanceMatrix(tfs,dmat)
  treeConstructor  = DistanceTreeConstructor(method = 'upgma')
  upgmaTree = treeConstructor.upgma(dm)
  Phylo.draw(upgmaTree)
  </code></pre>
  
  <p>where dmat is a lower triangle distance matrix, and tfs is a list of names that are used for columns/rows.  When looking at the bootstrapping examples, it seems like all of the input needs to be raw sequence data and not a distance matrix like I used above, does anyone know a workaround for this problem?
  Thanks!  </p>