The commenters seem to agree that this question is off topic. What specifically about the question makes it off-topic?
When it comes to a homework-y type question, I apply similar rules to a poster that I would as a TA to students:
Can you show me that you've thought about the assignment you're trying to solve by telling me how you would begin to approach the problem?
Can you show me that you're asking for help on what you're stuck with, rather than asking me to solve the whole problem for you?
Is it on topic?
I have X number of sequences, all the same lenght. For each pair of sequence I need to compute the alignment score based on the scheme: +1 = match, -2 = mis-match. I work in Perl, without using modules. Can anyone please tell me the guideline on how I should organize my program?
fails at least two of the three tests.
Asking for pseudocode or Perl code is off-topic, and the phrasing of the question (simple algorithm when better ones exist, no Perl modules) suggests a completing a whole homework problem without a whole lot of thought given to how to tackle it.
I think that the specific reason that the question is off-topic is that it only really asks "how should I structure my program?". Bioinformatics questions, and even homework-y questions should be on-topic (as long as they are about some specific aspect of the problem and not just "write code that does X for me").