Neighbor Joining Plus - algorithm for phylogenetic tree reconstruction with proper nodes assignment

TL;DR

This paper introduces Neighbor Joining Plus, an algorithm for phylogenetic tree reconstruction that allows for nodes with multiple offspring, providing a more flexible and accurate representation of evolutionary relationships.

Contribution

It extends existing phylogenetic algorithms to accommodate non-binary trees with internal nodes representing ancestors with multiple descendants.

Findings

Reconstructs non-binary phylogenetic trees with proper internal node assignment.

Simplifies derivation of evolutionary pathways and mutation analysis.

Extends existing algorithms for unbiased topologies.

Abstract

Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such assumptions forms therefore a binary tree, with all the nodes labeled as leaves. However, these constraints are unduly restrictive as there are numerous data sets with multiple offspring of the same ancestors. Here we propose a solution to analyze and visualize such sets in a more intuitive manner. The method reconstructs phylogenetic tree by assigning the sequences with offspring as internal nodes, and the sequences without offspring as leaf nodes. In the resulting tree there is no constraint for the number of adjacent nodes, which means that the solution tree needs not to be a binary graph only. The subsequent derivation of evolutionary pathways, and pair-wise mutations, are then an algorithmically straightforward, with edge's length corresponding directly to the number of mutations. Other tree reconstruction algorithms can be extended in the proposed manner, to also give unbiased topologies.