The source code of generating Top-1-grams is in the source code\psi folder. This program is dependent on the PSI-BLAST package. 
The executable file of this program for windows OS and input, output examples can be found in the binary\psi folder. The database for PSI-BLAST searching can be downloaded from ftp://ftp.ebi.ac.uk/pub/databases/nrdb90/. The users should format the database for PSI-BLAST searching. 
The source code of generating the distance-based feature vector is in the source code\feature folder. 
The executable file of this program for windows OS along with input and output examples can be found in the bin\feature folder.

Usage of the programs:
PSI usage: [program name] [input protein sequence file in FASTA format] [frequency profile output folder] [string of Top-1-grams in FASTA format]
FEATURE usage: [program name] [max distance] [input protein sequence file in FASTA format] [output feature vector file]

Here are examples of the command lines of the two programs for windows OS.
Psi.exe test.txt FrequencyProfile test_profile_seq.txt
feature.exe 50 Fasta.txt Output.txt
The input and output files can be found in the binary folder.