[BiO BB] A series of Pairwise alignments

[hamid]

  Hi buddy,
 Does anybody know how can I perform a series of pairwise alignments among 
all members of a set of proteins (almost 150 proteins) those I have their 
FastA sequences and sort mostly matched couples? I do not want to use 
ClustalW multiple alignment.
 Yours,
 Hamid

/*
 Hamid Nikbakht,
 M.Sc of Cell and Molecular Biology,
 Laboratory of Biophysics and Molecular Biology,
 Bioinformatics Center,
 Institute of Biochemistry and Biophysics(IBB),
 University of Tehran,
 Tehran,Iran.
 Tel: +98-21-6111-3322
 Fax: +98-21-6640-4680
 Alt. E-mail: nikbakht at ibb.ut.ac.ir
*/