These papers describe FastTree: the first paper describes FastTree 1.0,
and the second paper describes heuristic minimum-evolution SPR moves,
maximum-likelihood NNIs, and SH-like local supports. We have also
eliminated the O(N2) steps in the neighbor-joining phase, and
implemented maximum-likelihood NNI moves and SH-like supports (see the
ChangeLog).

Price, M.N., Dehal, P.S., and Arkin, A.P. (2009) FastTree: Computing
Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix.
Molecular Biology and Evolution 26:1641-1650, doi:10.1093/molbev/msp077.

Price, M.N., Dehal, P.S., and Arkin, A.P. (2010) FastTree 2 -- 
Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE,
5(3):e9490. doi:10.1371/journal.pone.0009490.