ComPhy: A Tool for Prokaryotic Phylogenies from Whole-Genome Data
Author Information
Author(s): Lin Guan Ning, Cai Zhipeng, Lin Guohui, Chakraborty Sounak, Xu Dong
Primary Institution: University of Missouri
Hypothesis
Can a new tool based on composite distance matrices improve the accuracy of prokaryotic phylogenetic analysis using whole-genome sequences?
Conclusion
ComPhy is a fast and robust tool for genome-wide inference of evolutionary relationships among genomes.
Supporting Evidence
- The method achieved above 90% agreement in quartet topologies with Bergey's taxonomy.
- ComPhy showed consistently better performance compared to several other phylogenetic analysis methods.
- The tool is fully automated and does not require multiple sequence alignment.
Takeaway
ComPhy helps scientists understand how different bacteria are related by looking at their entire genomes instead of just parts of them.
Methodology
The study used a composite distance matrix calculated from complete gene sets between genome pairs to produce a phylogenetic tree.
Potential Biases
Potential misclassification due to high rates of lateral gene transfer in some species.
Limitations
The method currently works only for single-chromosome species and does not account for lateral gene transfer.
Participant Demographics
398 single-chromosome prokaryotic genomes were analyzed.
Statistical Information
Statistical Significance
p<0.05
Digital Object Identifier (DOI)
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