Evolutionary biologists have introduced numerous statistical approaches to explore nonvertical evolution, such as horizontal gene transfer, recombination, and genomic reassortment, through collections of Markov-dependent gene trees. These tree collections allow for inference of nonvertical evolution, but only indirectly, making findings difficult to interpret and models difficult to generalize....

Ancestral sequence reconstruction (ASR) is widely used to formulate and test hypotheses about the sequences, functions, and structures of ancient genes. Ancestral sequences are usually inferred from an alignment of extant sequences using a maximum likelihood (ML) phylogenetic algorithm, which calculates the most likely ancestral sequence assuming a probabilistic model of sequence evolution and ...

Phylogenetic networks are a generalization of evolutionary or phylogenetic trees that are used to represent the evolution of species which have undergone reticulate evolution. In this paper we consider spaces of such networks defined by some novel local operations that we introduce for converting one phylogenetic network into another. These operations are modeled on the well-studied nearest-nei...

Modern phylogenetic studies may benefit from the analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome-scale analysis are believed to be more accurate than the gene-based alternative. However, the computational complexity of current phylogenomic procedures, inappropriateness of standard phylogenetic tools to process genome-wide data, and lack o...

Phylogenies are useful for organizing knowledge of biological diversity, for structuring classifications, and for providing knowledge of events that occurred during evolution. Different phylogenetic reconstruction techniques are available. In this paper Distance based technique is used. Distance measure is an important issue in phylogenetic analysis. Traditional approaches are time-consuming du...

The gene tree and species tree problem remains a central problem in phylogenomics. To overcome this problem, gene concatenation approaches have been used to combine a certain number of genes randomly from a set of widely distributed orthologous genes selected from genome data to conduct phylogenetic analysis. The random concatenation mechanism prevents us from the further investigations of the ...

Phylogenies are useful for organizing knowledge of biological diversity, for structuring classifications, and for providing knowledge of events that occurred during evolution. Different phylogenetic reconstruction techniques are available. In this paper Distance based technique is used. Distance measure is an important issue in phylogenetic analysis. Traditional approaches are time-consuming du...

In the computational biology area, my focus is on developing advanced computational approaches and tools to address grand challenges in understanding of biological systems and their impact on nature and human health. My dissertation research was on large scale phylogenetic inference, in which I have developed a high performance, Bayesian-based phylogenetic inference framework [1]. Part of the w...

We have developed a comprehensive gene orientated phylogenetic resource, EnsemblCompara GeneTrees, based on a computational pipeline to handle clustering, multiple alignment, and tree generation, including the handling of large gene families. We developed two novel non-sequence-based metrics of gene tree correctness and benchmarked a number of tree methods. The TreeBeST method from TreeFam show...