PHLAWD (pronounced flawd) allows for the creation of large (mega) phylogenies using NCBI databases. The code has been developed extensively over the last couple years.
- Smith, S. A. and M. J. Donoghue. 2008. Rates of Molecular Evolution are Linked to Life History in Flowering Plants. Science. pdf
- Smith, S. A., J. Beaulieu, and M. J. Donoghue. 2009. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evol. Biol. link