The amount of sequence data available to reconstruct the evolutionary history of genes and species has increased 20-fold in the past decade. Consequently the size of phylogenetic analyses has grown as well, and phylogenetic methods, algorithms and their implementations have struggled to keep pace. Computational and other challenges raised by this burgeoning database emerge at several stages of analysis, from the optimal assembly of large data matrices from sequence databases, to the efficient construction of trees from these large matrices and the piece-wise assembly of 'supertrees' from those trees in turn. A final challenge is posed by the difficulty of visualizing and making inferences from trees that might soon routinely contain thousands of species.