Next-generation phylogenomics

Chan, Cheong Xin and Ragan, Mark A. (2013) Next-generation phylogenomics. Biology Direct, 8 1: 3.1-3.14. doi:10.1186/1745-6150-8-3


Author Chan, Cheong Xin
Ragan, Mark A.
Title Next-generation phylogenomics
Journal name Biology Direct   Check publisher's open access policy
ISSN 1745-6150
Publication date 2013-01-22
Year available 2013
Sub-type Article (original research)
DOI 10.1186/1745-6150-8-3
Open Access Status DOI
Volume 8
Issue 1
Start page 3.1
End page 3.14
Total pages 14
Place of publication London, United Kingdom
Publisher BioMed Central
Collection year 2014
Language eng
Abstract Thanks to advances in next-generation technologies, genome sequences are now being generated at breadth (e.g. across environments) and depth (thousands of closely related strains, individuals or samples) unimaginable only a few years ago. Phylogenomics ? the study of evolutionary relationships based on comparative analysis of genome-scale data ? has so far been developed as industrial-scale molecular phylogenetics, proceeding in the two classical steps: multiple alignment of homologous sequences, followed by inference of a tree (or multiple trees). However, the algorithms typically employed for these steps scale poorly with number of sequences, such that for an increasing number of problems, high-quality phylogenomic analysis is (or soon will be) computationally infeasible. Moreover, next-generation data are often incomplete and error-prone, and analysis may be further complicated by genome rearrangement, gene fusion and deletion, lateral genetic transfer, and transcript variation. Here we argue that next-generation data require next-generation phylogenomics, including so-called alignment-free approaches.
Keyword Phylogenomics
Multiple sequence alignment
Alignment-free methods
k-mers
Homology signal
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Article no. 3

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2014 Collection
School of Chemistry and Molecular Biosciences
Institute for Molecular Bioscience - Publications
 
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Citation counts: TR Web of Science Citation Count  Cited 31 times in Thomson Reuters Web of Science Article | Citations
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Created: Fri, 01 Feb 2013, 17:59:16 EST by Cheong Xin Chan on behalf of School of Chemistry & Molecular Biosciences