I am working on a novel algorithm to calculate pairwise distance between nucleotide sequences and I am using those distances to construct phylogenetic trees.
I need to test the accuracy of my work comparing with benchmark trees (in literature) created using distance based methods, so I can validate my algorithm. Right now, I can find trees created based on character based methods but not for distance based methods.
There is an R package for this called treeclust
https://journal.r-project.org/archive/2015-2/buttrey-whitaker.pdf
You might use ALF - Artificial Life Framework, in which you can simulate gene trees, species trees as well as gene-sequences.
http://mbe.oxfordjournals.org/content/early/2011/12/12/molbev.msr268
The simulated sequences can be used for your distance based approach and your computed gene/species tree can then be compared with the original simulated ones.
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