When you code the script, you can have it change to the directory where the makefile.pl is located for all modules to be installed. Something like the following:

chdir "/root/shashi/msa-prereq/Tie-File-0.96/" or die "cannot chdir to
+ /root/shashi/msa-prereq/Tie-File-0.96/: $!";
system "Makefile.pl";
#other code
#other code 
chdir ""/root/shashi/msa-prereq" or die "Cannot chdir to "/root/shashi
+/msa-prereq: $!";
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Repeat the same code for all modules that need installed.

Edit:Updated to change back to /root/shashi/msa-prereq befor changing to the next module folder