Some years ago I was using that software for AFLP analysis, and then used a software called WinBoot for the bootstrap analysis. You can check more details here:
Article Preliminary assessment of AFLP fingerprinting of Rubus glauc...
https://sites.google.com/site/pbg804/winboot
In any case, I do believe that some R package can do both tasks! Maybe some else can recommend.
Actually, I tried many softwares but finally, I used Mesquite software for generating Newick file (with 100 permutations, UPGMA) then I uploaded that Newick file onto iTOL v6 for circular phylogenetic tree construction.