Tests For Neutrality On Large Datasets?

Question

[Dj1]

Are there any software tools that can test for selection at particular positions at a sequence which scale well to large datasets (several thousand sequences)?

Many dn/ds analysis tools don't seem to scale so well. For example, Hyphy seems to take a phylogenetic tree as input, and constructing a phylogenetic tree for several thousand sequences, while possible, requires more specialized tools.

Many of these tools don't seem to be designed for working on this many sequences (eg they take an inordinate amount of time to long time to load & run, or they crash). Even just calculating dnadist using phylip on this many sequences takes a long time.

[Joseph Hughes]

I have had similar problems but managed to sort it using Hyphy on the command line with a batch script that calculates a quick NJ tree, does modeltest and then runs the selection analysis to get the dN/dS.