Phylogenetic Memory

Trading Memory for Running Time in Phylogenetic Likelihood Computations

The revolution in wet-lab sequencing techniques that has given rise to a plethora of whole-genome or wholetranscriptome sequencing projects, often targeting 50 up to 1000 species, poses new challenges for efficiently computing the phylogenetic likelihood function both for phylogenetic inference and statistical post-analysis purposes. The phylogenetic likelihood function as deployed in maximum l...

Unrealistic phylogenetic trees may improve phylogenetic footprinting

Unrealistic phylogenetic trees may improve phylogenetic footprinting

Motivation The computational investigation of DNA binding motifs from binding sites is one of the classic tasks in bioinformatics and a prerequisite for understanding gene regulation as a whole. Due to the development of sequencing technologies and the increasing number of available genomes, approaches based on phylogenetic footprinting become increasingly attractive. Phylogenetic footprinting ...

Unrealistic phylogenetic trees may improve phylogenetic footprinting

Motivation The computational investigation of DNA binding motifs from binding sites is one of the classic tasks in bioinformatics and a prerequisite for understanding gene regulation as a whole. Due to the development of sequencing technologies and the increasing number of available genomes, approaches based on phylogenetic footprinting become increasingly attractive. Phylogenetic footprinting ...

Unrealistic phylogenetic trees may improve phylogenetic footprinting