Hi everyone, I have developed a new alignment free method to generate the phylogenetic tree from the Mitochondrial Genome sequences. I need to check the bootstrap supports of my newly generated trees. But I have doubt how can I bootstrap unaligned sequences and how to compute the final bootstrap scores for each clade of the tree. So in this regard, if you would suggest what should my approach to compute the confidence scores of our proposed method. Thanking you,

If your alignment-free approach is based on k-mers you can resample the original k-mers with replacement.

no its based on graphical method, representing a genome sequence graphically and computes the distance matrix.