Conclusion: We have briefly described the various methods that are available for phylogenetic tree construction. Over the years, researchers have encountered numerous number of ways for constructing phylogenetic tree.
Alignment free phylogenetic tree construction approaches overcome the overhead necessary with the alignment based approaches. And thus it is way faster than most other methods. We flag this as our motivation and use gamma model of rate heterogeneity from binary data produced by k-mer counting for constructing phylogenetic tree.
Our method is fast and from our result with simulated data, we have concluded that our method is at least as good as the GTRGAMMA approach with some constraints. This is great because one has to align the sequences first to use them with GTRGAMMA model. And with our method, we can find the same result without undergoing the sequence alignment overhead.
The constraints that we are making with our approach are that the branch length of sister taxa can not be too short (<0.01) or too long (>0.1). The reasons have already been described above. Future works may include to resolve these constraints and make our method to be more extensive.