Hi.... Running SAM is very simple, just run "sam allseqs.phy large.tre small.tre" the result will be be stored in the file "result" in the current directory. The two versions of SAM (linux x64 binaries) and the datasets mentioned in the paper are available for download:

Software Binaries
SAM-EVDownload
SAM-EDDownload

Datasets
Plants 500Download
Angiosperms processedDownload
MammalsDownload

If you still have any questions, feel free to contact me at: sheikh at the rate of cise dot ufl. e d u

Saad Sheikh