Abstract
Most methods for phylogenetic tree reconstruction are based on sequence alignments; they infer phylogenies based on aligned nucleotide or amino-acid residues. Gaps in alignments are usually not used as phylogenetic signal, even though they can, in principle, provide valuable information. In this paper, we explore an alignment-free approach to utilize insertions and deletions for phylogeny inference. We are using our previously developed approach Multi-SpaM, to generate local gap-free four-way alignments, so-called quartet blocks. For pairs of quartet blocks involving the same four sequences, we consider the distances between these blocks in the four sequences, to obtain hints about insertions or deletions that may have occurred since the four sequences evolved from their last common ancestor. This way, a pair of quartet blocks can support one of the three possible quartet topologies for the four involved sequences. We use this information as input for Maximum-Parsimony and for the software Quartet MaxCut to reconstruct phylogenetic trees that are only based on insertions and deletions.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Some additional test data; minor typos fixed; minor improvements in writing.