I have used python 3.6 and biopython 1.72 for viewing phylogenetiv trees. I have a protein msa file and a resulting tree file from the data. To evaluate the tree topology, I have generated a 1000 replicate trees for my data. In order to get branch support for my original tree with bootstrap replicates I have used following function;

def get_support(target_tree, trees, len_trees=None):
    """Calculate branch support for a target tree given bootstrap replicate trees.

    :Parameters:
        target_tree : Tree
            tree to calculate branch support for.
        trees : iterable
            iterable of trees used to calculate branch support.
        len_trees : int
            optional count of replicates in trees. len_trees must be provided
            when len(trees) is not a valid operation.

    """
    term_names = sortedterm.name
                        for term in target_tree.find_clades(terminal=True))
    bitstrs = {}

    size = len_trees
    if size is None:
        try:
            size = len(trees)
        except TypeError:
            raise TypeError("Trees does not support len(trees), "
                            "you must provide the number of replicates in trees "
                            "as the optional parameter len_trees.")

    for clade in target_tree.find_clades(terminal=False):
        bitstr = _clade_to_bitstr(clade, term_names)
        bitstrs[bitstr] = (clade, 0)
    for tree in trees:
        for clade in tree.find_clades(terminal=False):
            bitstr = _clade_to_bitstr(clade, term_names)
            if bitstr in bitstrs:
                c, t = bitstrs[bitstr]
                c.confidence = round ((t + 1) * 100.0 / size)
                bitstrs[bitstr] = (c, t + 1)
    return target_tree

The problem I am facing is that this function results a tree that shows branch support values for a few of the branches and not for all. I'm really stuck with this point and can't figure out what is the real problem?

Can anyone come up with a solution for this?