Alignment-free inference of hierarchical and reticulate phylogenomic relationships

Bernard, Guillaume, Chan, Cheong Xin, Chan, Yao-ban, Chua, Xin-Yi, Cong, Yingnan, Hogan, James M., Maetschke, Stefan R. and Ragan, Mark A. (2017) Alignment-free inference of hierarchical and reticulate phylogenomic relationships. Briefings in Bioinformatics, . doi:10.1093/bib/bbx067


Author Bernard, Guillaume
Chan, Cheong Xin
Chan, Yao-ban
Chua, Xin-Yi
Cong, Yingnan
Hogan, James M.
Maetschke, Stefan R.
Ragan, Mark A.
Title Alignment-free inference of hierarchical and reticulate phylogenomic relationships
Journal name Briefings in Bioinformatics   Check publisher's open access policy
ISSN 1477-4054
1467-5463
Publication date 2017-06-30
Sub-type Article (original research)
DOI 10.1093/bib/bbx067
Open Access Status DOI
Total pages 10
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Language eng
Abstract We are amidst an ongoing flood of sequence data arising from the application of high-throughput technologies, and a concomitant fundamental revision in our understanding of how genomes evolve individually and within the biosphere. Workflows for phylogenomic inference must accommodate data that are not only much larger than before, but often more error prone and perhaps misassembled, or not assembled in the first place. Moreover, genomes of microbes, viruses and plasmids evolve not only by tree-like descent with modification but also by incorporating stretches of exogenous DNA. Thus, next-generation phylogenomics must address computational scalability while rethinking the nature of orthogroups, the alignment of multiple sequences and the inference and comparison of trees. New phylogenomic workflows have begun to take shape based on so-called alignment-free (AF) approaches. Here, we review the conceptual foundations of AF phylogenetics for the hierarchical (vertical) and reticulate (lateral) components of genome evolution, focusing on methods based on k-mers. We reflect on what seems to be successful, and on where further development is needed.
Keyword D2 statistics
TF–IDF
Alignment-free
k-mer
Lateral genetic transfer
Phylogenomics
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
School of Chemistry and Molecular Biosciences
 
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Created: Fri, 07 Jul 2017, 11:29:18 EST by Mrs Louise Nimwegen on behalf of School of Chemistry & Molecular Biosciences