Dear Sorouhesh,
Yes, there is a command"Subgroups" for that in GAP package "sonata".So first 
you will have to load that as following:
gap> LoadPackage("sonata");;
gap> s5:=SymmetricGroup(IsPermGroup,5);

Sym( [ 1 .. 5 ] )
gap> Subgroups(s5);
HERE YOU WILL GET THE LIST OF ALL THE SUBGROUPS OF s5
gap> Size(last);
156
THERE ARE 156 SUBGROUPS OF s5
similarly for s6
gap> s6:=SymmetricGroup(IsPermGroup,6);

Sym( [ 1 .. 6 ] )
gap> Subgroups(s6);
gap> Size(last);
1455
Cheers,
Muhammad Shah

> Date: Wed, 28 Mar 2012 17:35:17 +0430
> From: msorouh...@gmail.com
> To: fo...@gap-system.org
> Subject: [GAP Forum] Transitive groups
> 
> Dear friends,
> 
> Kindly asking: Can we ask GAP to list all subgroups of a group, for example
> S5 or S6?
> 
> Best
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