Sampling motifs on phylogenetic trees

Sampling motifs on phylogenetic trees.

We present a method to find motifs by simultaneously using the overrepresentation property and the evolutionary conservation property of motifs. This method is applicable to divergent species where alignment is unreliable, which overcomes a major limitation of the current methods. The method has been applied to search regulatory motifs in four yeast species based on ChIP-chip data in Saccharomy...

Algorithms on Phylogenetic Trees

Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees.

Bertrand, Y., and M. Härlin. 2006. Stability and universality in the application of taxon names in phylogenetic nomenclature. Syst. Biol. 55:848–858. Bininda-Emonds, O. R. P. 2004. The evolution of supertrees. Trends Ecol. Evol. 19:315–322. Bryant, H. N., and P. D. Cantino. 2002. A review of criticisms of phylogenetic nomenclature: Is taxonomic freedom the fundamental issue? Biol. Rev. 77:39–55...

An Optimization-Based Sampling Scheme for Phylogenetic Trees

Much modern work in phylogenetics depends on statistical sampling approaches to phylogeny construction to estimate probability distributions of possible trees for any given input data set. Our theoretical understanding of sampling approaches to phylogenetics remains far less developed than that for optimization approaches, however, particularly with regard to the number of sampling steps needed...

On Symmetries in Phylogenetic Trees

Billey et al. [arXiv:1507.04976] have recently discovered a surprisingly simple formula for the number an(σ) of leaf-labelled rooted nonembedded binary trees (also known as phylogenetic trees) with n ≥ 1 leaves, xed (for the relabelling action) by a given permutation σ ∈ Sn. Denoting by λ ` n the integer partition giving the sizes of the cycles of σ in non-increasing order, they show by a guess...