>Neighbor Joining is NOT a good tree building method. If you change the order o
f
>input of taxa, you change the tree.
Mark,
What is your reference for this statement? I have "built" lots of neighbor-
joining tress using both MEGA and other programs and have never found this to
be true. Also, someone mentioned that distances assume rate constancy. That
is not true. Some tree-building algorithms (UPGMA) do, but that is different.
Neighbor joining certainly allows different rates of evolution in different
lineages.
Carla Hass
Biology
Penn State
