How much local storage does it normally take?

[yenagra]

Just wonder if I need to enlarge my harddrive before running this program.

[arendsee]

@yenagra I wouldn't worry about the harddrive. phylostratr only uses proteomes and these tend to only require tens of megabytes. So as long as you have a few free GB, you will be fine.

You are far more likely to run into memory problems. I can just barely run Arabidopsis thaliana test case on my desktop, where I have 8 GB of RAM. So currently you may need to run phylostratr on a server if you are doing a large study.

There is certainly a lot of room for improvement in the phylostratr implementation. I could replace the in-memory data structures with a SQLite database. That would basically solve the memory problem.

The other performance issue to consider is the time required to BLAST everything. You will likely want to run the BLASTs on a server and phylostratr currently doesn't automate this. Though handling high-performance computation in R is totally possible.

[yenagra]

That's good, thanks.