I have a library of ~2000 nucleotide sequences for which I'd like to visualize the similarity. Because some of the sequences are very diverse, its not feasible to perform a multiple sequence alignment and then build a phylogenetic tree, as (at least when I perform this process using MEGA) no common bases can be found.
I'm looking for a way to build a phylogenetic tree based on individual pairwise distances between each pair of sequences (aligned in isolation), and not on the pairwise distances of sequences taken from a multiple alignment. Building a tree this way should overcome the issue of some sequences not being aligned due to their extreme diversity.
Alternatively, I'd like to create a plot where distances between two points are proportional to the pairwise distances between the sequences they represent. In this way, I could start to visually identify clusters of sequences which might exist.