Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs

We present kleuren, a novel assembly-free method to reconstruct phylogenetic trees using the Colored de Bruijn Graph. kleuren works by constructing the Colored de Bruijn Graph and then traversing it, finding bubble structures in the graph that provide phylogenetic signal. The bubbles are then aligned and concatenated to form a supermatrix, from which a phylogenetic tree is inferred. We introduce the algorithms that kleuren uses to accomplish this task, and show its performance on reconstructing the phylogenetic tree of 12 Drosophila species. kleuren reconstructed the established phylogenetic tree accurately, and is a viable tool for phylogenetic tree reconstruction using whole genome sequences. Software package available at: https://github.com/Colelyman/kleurenComment: 6 pages, 3 figures, accepted at BIBE 2017. Minor modifications to the text due to reviewer feedback and fixed typo

When two trees go to war

Rooted phylogenetic networks are often constructed by combining trees, clusters, triplets or characters into a single network that in some well-defined sense simultaneously represents them all. We review these four models and investigate how they are related. In general, the model chosen influences the minimum number of reticulation events required. However, when one obtains the input data from two binary trees, we show that the minimum number of reticulations is independent of the model. The number of reticulations necessary to represent the trees, triplets, clusters (in the softwired sense) and characters (with unrestricted multiple crossover recombination) are all equal. Furthermore, we show that these results also hold when not the number of reticulations but the level of the constructed network is minimised. We use these unification results to settle several complexity questions that have been open in the field for some time. We also give explicit examples to show that already for data obtained from three binary trees the models begin to diverge

SunStar: an implementation of the generalized STAR method

Master's Project (M.S.) University of Alaska Fairbanks, 2017STAR ... is a method of computing species trees from gene trees. Later, STAR was generalized and proven to be statistically consistent given a few conditions (Allman, Degnan, and Rhodes 2013). Using these conditions, it is possible to investigate robustness in the species tree inference process, the lack of which will produce instabilities in the tree resulting from STAR. We have developed a software package that estimates support for inferred trees called SunStar