Pplacer: A Tool for Phylogenetic Placement of Sequences
Author Information
Author(s): Matsen Frederick A, Kodner Robin B, Armbrust E Virginia
Primary Institution: Fred Hutchinson Cancer Research Center
Hypothesis
Can likelihood-based phylogenetic methods be adapted for large volumes of short reads from next-generation sequencing?
Conclusion
Pplacer enables efficient phylogenetic placement and visualization, making likelihood-based phylogenetics practical for large collections of reads.
Supporting Evidence
- Pplacer can place twenty thousand short reads on a reference tree of one thousand taxa per hour per processor.
- The software provides visualizations using branch thickness and color to represent the number of placements and their uncertainty.
- A simulation study using reads generated from 631 COG alignments shows a high level of accuracy for phylogenetic placement.
Takeaway
Pplacer is a software that helps scientists place DNA sequences on a tree to understand their relationships, even when they have short pieces of DNA.
Methodology
Pplacer uses a fixed reference tree and alignment to place query sequences, calculating posterior probabilities and likelihoods for placements.
Limitations
Pplacer is not a substitute for traditional phylogenetic analysis and may not perform well with very distant taxa.
Digital Object Identifier (DOI)
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