Dissimilarities in alignment-free methods for phylogenetic analysis based on genomes

Chen, Xiao-Su, Yu, Zuguo, & Zheng, Juan (2014) Dissimilarities in alignment-free methods for phylogenetic analysis based on genomes. Current Bioinformatics, 9(3), pp. 218-227.

View at publisher

Abstract

Whole genome sequences are generally accepted as excellent tools for studying evolutionary relationships. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignments could not be directly applied to the whole-genome comparison and phylogenomic studies. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. The “distances” used in these alignment-free methods are not proper distance metrics in the strict mathematical sense. In this study, we first review them in a more general frame — dissimilarity. Then we propose some new dissimilarities for phylogenetic analysis. Last three genome datasets are employed to evaluate these dissimilarities from a biological point of view.

Impact and interest:

0 citations in Scopus
Search Google Scholar™

Citation counts are sourced monthly from Scopus and Web of Science® citation databases.

These databases contain citations from different subsets of available publications and different time periods and thus the citation count from each is usually different. Some works are not in either database and no count is displayed. Scopus includes citations from articles published in 1996 onwards, and Web of Science® generally from 1980 onwards.

Citations counts from the Google Scholar™ indexing service can be viewed at the linked Google Scholar™ search.

ID Code: 88579
Item Type: Journal Article
Refereed: Yes
Keywords: Alignment-free method, dissimilarity, distance, genome, phylogenetic analysis.
DOI: 10.2174/1574893609999140523124702
ISSN: 1574-8936
Divisions: Current > QUT Faculties and Divisions > Science & Engineering Faculty
Deposited On: 08 Nov 2015 23:47
Last Modified: 08 Nov 2015 23:47

Export: EndNote | Dublin Core | BibTeX

Repository Staff Only: item control page