Phylogenetic and Phylogenomic Analyses for Large Datasets

  • Lê Sỹ Vinh University of Engineering and Technology, Vietnam National University, Hanoi
Keywords: DNA sequence, evolutionary relationship, senome, phylogenetics, phylogenomics, large dataset, protein sequence


The phylogenetic tree is a main tool to study the evolutionary relationships among species. Computational methods for building phylogenetic trees from gene/protein sequences have been developed for decades and come of age. Efficient approaches, including distance-based methods, maximum likelihood methods, or classical maximum parsimony methods, are now able to analyze datasets with thousands of sequences. The advanced sequencing technologies have resulted in a huge amount of data including whole genomes. A number of methods have been proposed to analyze the wholegenome datasets, however, numerous challenges need to be addressed and solved to translate phylogenomic inferences into practices. In this paper, we will analyze widely-used methods to construct large phylogenetic trees, and available methods to build phylogenomic trees from whole-genome datasets. We will also give recommendations for best practices when performing phylogenetic and phylogenomic analyses. The paper will enable researchers to comprehend the state-ofthe-art methods and available software to efficiently study the evolutionary relationships among species from large datasets.

Author Biography

Lê Sỹ Vinh, University of Engineering and Technology, Vietnam National University, Hanoi

Le Sy Vinh obtained PhD in Bioinformatics from Heinrich Heine University, Duesseldorf, Germany 2005, subsequently followed a postdoc fellowship at American Museum of Natural History, NYC from 2005 to 2008. He is currently the Dean of the Faculty of Information Technology, University of Engineering and Technology, Vietnam National University, Hanoi. Le Sy Vinh is an expert in phylogenetic analysis, the author of widely-used software such as IQPNNI, POY4, UFBoot2. He is the group leader of many human genome projects in Vietnam including the first Vietnamese human genome, building the comprehensive Vietnamese human genome database, or Autism spectrum disorder in Vietnamese children.

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