Viral Qausispecies analysis- tips and tricks? PLEASE HELP!

[CrazyCoV]

So my project, which was NOT supposed to be bioinformatic, has turned into a bioinformatics things.
Does ANYONE here have suggestions on how to best quantify and analyze viral quasispecies subpopulations?
And, full disclosure, I am HORRIBLE at programming. I learn quick, but it is not a strong skill for me.
I can't find a GUI interface for any of the quasispecies software. So ANY help on coding and how to make things run and run easier would be greatly appreciated.
So any comments? VisPa? QuRe? I have tried just running Samtools SNP caller, but it says I don't have any variants....but I do. Because I can see them in CLC. i just don't know how to make CLC give me the information. Plus CLC is so resource intensive it keeps crashing out on me.
PLEASE HELP ME!!

[gringer]

I recommend harrassing CLC support until you get your money's worth out of that software; just relax and let them do the coding side of things for you. If it costs as much as an entry-level bioinformatician to run, you should really be able to survive without any bioinformatics skills to use it and interpret the results.

On a lighter note...

Does ANYONE here have suggestions on how to best quantify and analyze viral quasispecies subpopulations?

I'm not familiar with how all the buzzwords you've used relate to the railway station, but you might get a better response by using the magic word "metagenomics". A brief search on the goggle brings up the following webber:

http://metagenomics.anl.gov/

Maybe that will be useful for you? I've seen it mentioned on SeqAnswers a bit, but am not familiar enough with metagenomics to say whether or not it would be good. Unfortunately, anything metagenomic is going to need bioinformatics skills and a bit of paper reading.

[A.N.Other]

I think you're probably going to need a slightly more specialist tool than CLC to get you through this.

I suggest you also look over ShoRAH (Zagordi(2011)Bioinformatics) and V-Phaser (Macalalad(2012)PLoS Comp Biol).