An Ultrafast Tool for Minimum Reticulate Networks

An Ultrafast Tool for Minimum Reticulate Networks

Due to hybridization events in evolution, studying different genes of a set of species may yield two or more related but different phylogenetic trees for the set of species. In this case, we want to combine the trees into a reticulate network with the fewest hybridization events. In this article, we develop a software tool (named UltraNet) for several fundamental problems related to the constru...

SOAP2: an improved ultrafast tool for short read alignment

SUMMARY SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy for indexing the reference sequence in the main memory. We tested it on the whole human genome and found th...

Reconstruction of Reticulate Networks from Gene Trees

One of the simplest evolutionary models has molecular sequences evolving from a common ancestor down a bifurcating phylogenetic tree, experiencing point-mutations along the way. However, empirical analyses of different genes indicate that the evolution of genomes is often more complex than can be represented by such a model. Thus, the following problem is of significant interest in molecular ev...

Minimum Field Strength in Ultrafast Magnetization Reversal

Close lower and upper bounds for the minimum reticulate network of multiple phylogenetic trees

MOTIVATION Reticulate network is a model for displaying and quantifying the effects of complex reticulate processes on the evolutionary history of species undergoing reticulate evolution. A central computational problem on reticulate networks is: given a set of phylogenetic trees (each for some region of the genomes), reconstruct the most parsimonious reticulate network (called the minimum reti...