My version of neighbor-joining in Python

I finished debugging my version of the neighbor-joining method in Python. The zipped project files are here. I also made an nj tree from the same data using PyCogent, ape, and Phylip's neighbor. Everybody agrees!

One last thing I haven't done is to write the code to assemble the tree's representation. What I actually have is a list of internal nodes with distances to their child nodes. There's always something more to do.

PyCogent:

edge.0 A:1.0; edge.0 B:4.0; edge.1 C:2.0; edge.2 F:4.75; root D:2.75; root E:2.25; edge.2 edge.1 1.25 edge.2 edge.0 2.25 edge.1 edge.0 1.0 root edge.2 0.75 root edge.1 2.0 root edge.0 3.0 ((((A:1.0,B:4.0):1.0,C:2.0):1.25,F:4.75):0.75,D:2.75,E:2.25);

Phylip:

Between And Length ------- --- ------ 1 B 4.00000 1 2 1.00000 2 C 2.00000 2 4 1.25000 4 3 0.75000 3 E 2.25000 3 D 2.75000 4 F 4.75000 1 A 1.00000 (B:4.00000,(C:2.00000,((E:2.25000,D:2.75000):0.75000,F:4.75000):1.25000):1.00000,A:1.00000);

ape:

> tr$edge.length [1] 2.25 2.75 0.75 1.25 1.00 1.00 4.00 2.00 4.75 > tr$edge [,1] [,2] [1,] 7 5 [2,] 7 4 [3,] 7 8 [4,] 8 9 [5,] 9 10 [6,] 10 1 [7,] 10 2 [8,] 9 3 [9,] 8 6 > tr$tip.label [1] "A" "B" "C" "D" "E" "F" (E:2.25,D:2.75,(((A:1,B:4):1,C:2):1.25,F:4.75):0.75);

me:

0 : B 4.000 A 1.000 1 : C 2.000 0 1.000 2 : E 2.250 D 2.750 3 : 1 1.250 2 0.750 F 4.75