Dear Sarah,

There is not a built-in .BF to do this (you can compute all pairwise tip-tip distances from the tree viewer, but that will not include ancestral sequences). You can right a very simple post-processor module (to drop into UserAddIns and be accessible via the console gears button), which would use the command:

Code:

BranchLength(tree,"node1;node2");
 

to compute the cumulative branch length between any nodes in the tree.
Here's a little working code example

Code:

function getAllPairwiseBranchLengths (treeID)
{
	ExecuteCommands ("allBranches = BranchName("+treeID+",-1);");
	_branchCount = Columns(allBranches)-1;
	outString = "";
	outString * 128;
	outString * "Node1,Node2,Distance";
	for (_b1 = 0; _b1 < _branchCount; _b1 = _b1+1)
	{
		bn1 = allBranches[_b1];
		for (_b2 = _b1+1; _b2 < _branchCount; _b2 = _b2+1)
		{
			bn2 = allBranches[_b2];
			ExecuteCommands ("bl=BranchLength("+treeID+",\""+bn1+";"+bn2+"\");");
			outString * ("\n"+bn1+","+bn2+","+bl);
		}
	}
	outString * 0;
	return outString;
}


Tree t = ((a:0.1,b:0.2)anc1:0.2,c:0.05,d:0.125);
fprintf (stdout, getAllPairwiseBranchLengths ("t"));
 

Cheers,
Sergei