Proper distance metrics for phylogenetic analysis using complete genomes without sequence alignment
| Autor: | Guo-Sheng Han, Zu-Guo Yu, Xiao-Wen Zhan, Vo Anh, Ka Hou Chu, Roger Wei Wang |
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| Rok vydání: | 2010 |
| Předmět: |
complete genome
Sequence alignment Genomics Biology Network topology Bioinformatics Genome Catalysis Article Inorganic Chemistry lcsh:Chemistry Phylogenetics Animals Point (geometry) composition vector Physical and Theoretical Chemistry Molecular Biology lcsh:QH301-705.5 Spectroscopy Phylogeny Phylogenetic tree correlation-related distance metric phylogenetic analysis Organic Chemistry General Medicine Computer Science Applications lcsh:Biology (General) lcsh:QD1-999 Algorithm Sequence Alignment Distance matrices in phylogeny Algorithms Genome Bacterial Genome Plant |
| Zdroj: | International Journal of Molecular Sciences International Journal of Molecular Sciences, Vol 11, Iss 3, Pp 1141-1154 (2010) Volume 11 Issue 3 Pages 1141-1154 |
| ISSN: | 1422-0067 |
| Popis: | A shortcoming of most correlation distance methods based on the composition vectors without alignment developed for phylogenetic analysis using complete genomes is that the “distances” are not proper distance metrics in the strict mathematical sense. In this paper we propose two new correlation-related distance metrics to replace the old one in our dynamical language approach. Four genome datasets are employed to evaluate the effects of this replacement from a biological point of view. We find that the two proper distance metrics yield trees with the same or similar topologies as/to those using the old “distance” and agree with the tree of life based on 16S rRNA in a majority of the basic branches. Hence the two proper correlation-related distance metrics proposed here improve our dynamical language approach for phylogenetic analysis. |
| Databáze: | OpenAIRE |
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