I am looking for easy to use bioinformatic software.

My research questions are mostly about having a few amplicons (from a known region) sequenced (with illumina). Within these samples, we pool the amplicons of different genotypes with a trait of interest in one pool and amplicons of genotypes without the trait of interest in the other pool. After mapping of the reads to a reference sequence, the nucleotide distribution is calculated for each position. After comparing the nucleotide distributions between the pools with and without the trait, candidate SNP's an be detected.

I have used the Lasergene NGEN package of DNASTAR for this approach in the past, using a trial version of this softare.

Can anyone recomment me software to follow a similar approach? We can purchase the license of DNASTAR but it is rather expensive.

Also, I am not a trained bioinformatician. I do need the easy-to-use interface and easy steps like in DNASTAR.

Thnx

Maarten