All Title Author
Keywords Abstract

Publish in OALib Journal
ISSN: 2333-9721
APC: Only $99

ViewsDownloads

Relative Articles

More...

Next-generation phylogenomics

DOI: 10.1186/1745-6150-8-3

Keywords: Phylogenomics , Multiple sequence alignment , Alignment-free methods , k-mers , Homology signal

Full-Text   Cite this paper   Add to My Lib

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. Reviewers Reviewed by Mr Alexander Panchin (nominated by Dr Mikhail Gelfand), Dr Eugene Koonin and Prof Peter Gogarten. For the full reviews, please go to the Reviewers’ comments section.

Full-Text

comments powered by Disqus

Contact Us

service@oalib.com

QQ:3279437679

WhatsApp +8615387084133

WeChat 1538708413