Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis.
Yang B, Wang Y, Qian PY
BMC Bioinformatics. 2016. doi: 10.1186/s12859-016-0992-y
COMMENT: In this publication the authors analyze the best regions regions for representing the full-length 16S genes in the phylogenetic analysis. They check the geodesic distance between the phylogenetic trees generated with different pairs of variable regions. The trees are built only until the phylum level and the geodesic distance is only considered at this level.
Other authors previously used algorithms for comparing phylogenetic trees and defining a distance between their topologies:
The authors conclude that V4-V6 appear to be the most reliable regions for representing the full-length 16S rRNA sequences for phylum rank classification, while V2 and V8 were the least reliable regions.