For each of several genomes, apart from the already available fasta sequence and associated GFF3 annotation files, I have also generated 5 additional GFF files for start-stop coordinates of 5 additional types of genomic features. 

My goal is four-fold in the context of these 6 GFF files and 1 genomic DNA sequence.

1. **Explore** where two or more of these genomic features overlap / intersect / co-localize - I am doing this via text manipulation, using bedtools overlap or bedtools intersect. But I want to visualize 2 or more tracks , and just text-based calculation of intersection is not satisfying during exploration phase. I want to visualize it.

2. Generate **high-detail images** (with flexibility of color / shapes like that in IGB or gff2ps) for **small intervals**, looking at specific and most interesting cases.

3. Generate **overview images** for **entire** chromosomes or even a **genome**, for overlap across these 6 types of genomic features , without confusing or overwhelming the reader.

4. Finally, to request advice on which tool and/or which **statistical test** to perform for verifying whether the observed physical **co-localization** of any 2 of the 6 types of genomic features is random or **non-random**. And if latter is true, are there more sophisticated tests to examine physical distribution of genomic loci types, relative to one another? And are there tests that can examine more than 2 types of genomic features at a time?

The rather old thread at https://www.biostars.org/p/363/ discusses answers to questions 1 - 3 above, but I am curious to know if there are better / updates tools for my goals than the ones I mentioned above or at the link (bedtools or bedOps, IGB, GBrowse, GFF2PS). Thanks!
You could do this (I think) with [Artemis][1] and/or the [Artemis Comparison Tool][2].

Load up the sequence, and read in the different annotation files and you can view them all together in the same window I believe.

It probably doesn't solve *all* of your requests though, but worth a look I think.


  [1]: https://www.sanger.ac.uk/science/tools/artemis
  [2]: https://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act