Discord among the gene trees of multilocus data has motivated the development of phylogenetic approaches that account for gene-tree heterogeneity in the estimation procedure. Rather than equating a gene tree with the phylogenetic history, the new approaches explicitly consider the relationships between gene trees and the underlying history of species divergence, providing direct estimates of sp...

Increased phylogenetic information (often based on analyses of DNA sequences) has revolutionized comparative biology. Phylogenies are used to guide the choice of species for comparisons and to identify traits that are homologous versus analogous. They are also used to perform “phylogenetically correct” statistical analyses that attempt to account for the fact that related species tend to resemb...

Up to now, various approaches for phylogenetic analysis have been developed. Almost all of them put stress on analyzing nucleic acid sequences or protein primary structures. In this paper, we take the physicochemical properties of amino acids into account and introduce the protein feature sequences into phylogenetic analysis by using the Bhattacharyya distance. We find that this method is effec...

Prolamin, the alcohol-soluble seed storage protein is major in many cereals. Foxtail millet (Setaria italica) contains prolamin (Setarin) as protein, which accounts > 50% of total protein. To in-silico characterize proteins foxtail millet, sequence coding for 14.3 kDa, 20.4 22 22.4 kDa and 26 were retrieved from NCBI database. Protein physio-chemical characterization was done through Protparam ...

Supertree methods combine multiple phylogenetic trees to produce the overall best "supertree." They can be used to combine phylogenetic information from datasets only partially overlapping and from disparate sources (like molecular and morphological data), or to break down problems thought to be computationally intractable. Some of the longest standing phylogenetic conundrums are now being brou...

Gene function annotation is important for a variety of downstream analyses genetic data. But experimental characterization remains costly and slow, making computational prediction an endeavor. Phylogenetic approaches to have been developed, but implementation practical Bayesian framework parameter estimation outstanding challenge. We developed computationally efficient model evolution gene anno...

Recently there has been renewed interest in phylogenetic inference methods based on phylogenetic invariants, alongside the related Markov invariants. Broadly speaking, both these approaches give rise to polynomial functions of sequence site patterns that, in expectation value, either vanish for particular evolutionary trees (in the case of phylogenetic invariants) or have well understood transf...