The Standford Graphbase is very good, with programs and documentations available.

Hey, thanks for the link! Sage is very good except that it's not windows native. :(

I've got my answer. And, the answer is YES. Mathematica or Python. Nothing else. Both of these have very high level data types and operations, that won't cripple you to implementation details. Thanks All

@JonAwbrey : You meant I should emphasize on theory and pencils?? Thanks

@Noldorin : Well but there many GA approaches to solve GT problems.

@baudolino : The book's free. But the software is not. They don't provide Graph Algorithms in the free edition. ;( Advanced graph related tools are included in 'Researcher' edition.

Well it seems promising! Specially, the accompanying free book. Let, me study more before I get you accepted. :P

sagemath excels here.

well, i'm a newbie. and i really don't know what to do! i just know there are several existing solutions to the problem i'm dealing with. and i need to implement and compare them. how? i don't know. i saw a book on all those optimization algos using MATLAB. and found mathematica have combinatorica as a special graph theory package consisting 450 function. like it a random graph generator function. so i can create random graphs with it and then run those optimization algos on these graphs and see what happen. but creation and visualization of user defined graphs in combinatorica is hard.

thanks for the share. sagemath.org includes this package too. but, as you wrote I have to be really good to do anything useful

@Jon : Nope! I need to experiment theorems with a sufficient enough tool, that will not boggle me down to it's acronyms. :) Update: Sagemath is free and has GT packages. But, again, my internet is too slow to download all that 2 GB! :'(

Thanks. jGraphT is good too. But, I'm too newbie to use it. They use generics and all sort of java acronyms. I wish I could have some tool, that would let me keep my concentration on GT, not on it's implementation.