Running the program at the Linux terminal

You should call the sequence alignment program in the following way. Once you have opened the linux terminal, you must type:

$ ./terminal.pl sequence1.txt sequence2.txt matrix.txt gap_penalty

where
  1. sequence1.txt: It is a .txt file in which sequence1 is recorded in fasta format
  2. sequence2.txt: It is another .txt file with sequence2 in fasta format
  3. matrix.txt: In this .txt file there is the substitution matrix. You can download one of the following:

    PAM30
    PAM70
    BLOSUM62
    BLOSUM80
  4. gap_penalty: You can write down any value you want (i.e. -4)

WARNING: If you can't run the program, maybe it's because you need to change the execution permission. To solve the problem, type:

$ chmod u+x name_of_program.pl

Afterwards, just type the calling instructions as indicated above.
Download the program
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Universitat Pompeu Fabra 2002