Fix buildNewick Formula and Update Dendrogram Branch Representation

[kylacochrane]

This PR (currently indirectly) addresses ISSUE13.

Changes:

• Fixed the buildNewick formula to adjust branch lengths (both internal and leaf branches) to represent cophenetic distances rather than patristic distances.
• Branch lengths now reflect the distance from all samples to their most recent common ancestor.

Benefits:

• This approach mirrors how BioNumerics currently displays dendrograms.
• It aligns with how GAS's fcluster generates flat clusters based on user-provided thresholds, ensuring the dendrogram allows users to visually interpret cluster levels by assessing branch heights between clusters.

Key Considerations:
This method deviates from the traditional representation of distances in dendrograms. As noted in ISSUE13, branch lengths are typically represented by patristic distances along a tree typically correspond to the values in the distance matrix (i.e., the sum of branch lengths from Sample A to Sample B should equal the distance provided in the matrix).

To align buildNewick with this traditional approach, the formula can be updated with the following adjustments:

def buildNewick(self,node, newick, parentdist, leaf_names):
        if node.is_leaf():
            return "%s:%f%s" % (leaf_names[node.id], (parentdist - node.dist / 2), newick)
        else:
            if len(newick) > 0:
                newick = f"):{(parentdist - node.dist/2)}{newick}"
            else:
                newick = ");"
            newick = self.buildNewick(node.get_left(), newick, node.dist, leaf_names)
            newick = self.buildNewick(node.get_right(), ",%s" % (newick), node.dist, leaf_names)
            newick = "(%s" % (newick)
            return newick