FASTA program discussion list

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Hi all,
I would like to slightly modify FASTA in order to accomplish two goals:

1) Making it read two FASTA files (e.g. test_file and library_file) and try to
pairwise align them this way:
sequence #1 of test_file ------- sequence #1 in library file
sequence #2 of test_file ------- sequence #2 in library_file 

So each sequence of test_file with the one in the correspondent position in
library_file

2) Strip down the output as much as possible, printing out the top alignment
only, without any headers or stats.

Could anyone point me to the section(s) of the code that I should modify in
order to achieve this?

Thank you.

Mauro