pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

By M. E T H O D O L O G Y A R T I C, Frederick Albert Matsen IV, Robin B. Kodner, V. Armbrust. 2010

1,025 citations recorded by the source corpus.

BackgroundLikelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-based phylogenetic methods cannot be applied to large volumes of short reads from next-generation sequencing due to computational complexity issues and lack of phylogenetic signal. "Phylogenetic placement," where a reference tree is fixed and the unknown query sequences are placed onto the tree via a reference alignment, is a way to bring the inferential power offered by likelihood-based approaches to large data sets.ResultsThis paper introduces pplacer, a software package for phylogenetic placement and subsequent visualization. The algorithm can place twenty thousand short reads on a reference tree of one thousand taxa per hour per processor, has essentially linear time and memory complexity in the number of reference taxa, and is easy to run in parallel. Pplacer features calculation of the posterior probability of a placement on an edge, which is a statistically rigorous way of quantifying uncertainty on an edge-by-edge basis. It also can inform the user of the positional uncertainty for query sequences by calculating expected distance between placement locations, which is crucial in the estimation of uncertainty with a well-sampled reference tree. The software provides visualizations using branch thickness and color to represent 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 over a wide range of alignment diversity, and the power of edge uncertainty estimates to measure placement confidence.ConclusionsPplacer enables efficient phylogenetic placement and subsequent visualization, making likelihood-based phylogenetics methodology practical for large collections of reads; it is freely available as source code, binaries, and a web service.

Subfields: Molecular Biology, Paleontology

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Citations in the corpus

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability (2013, methodology): “We selected these default parameters based on an expectation that, if the program works well for difﬁcult (distantly related) cases, it should also work well for easy cases.”
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes (2013, methodology): “HMMALIGN was used to align metagenomic sequences on the reference alignments and Pplacer (Matsen et al., 2010) was used to map the sequences in the reference trees using the Bayesian option.”
Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm (2012, methodology): “Our new method, called PAGAN, infers ancestral sequences for the reference alignment and adds new sequences in their phylogenetic context, either to predefined positions or by finding the best placement for sequences of unknown origin.”
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees (2016, methodology): “jplace files (11) created by EPA (12) or pplacer (13).”
PhyloSift: phylogenetic analysis of genomes and metagenomes (2014, methodology): “256 PhyloSift employs pplacer [37] for this task.”
Interactive Tree Of Life (iTOL) v4: recent updates and new developments (2019, background): “Phylogenetic placements files created by EPA (11) and pplacer (12) are also supported.”
Influenza Research Database: An integrated bioinformatics resource for influenza virus research (2016, methodology): “This algorithm constructs an HA reference tree and then applies the pplacer method (19) to place the query sequence into the reference tree, thus identifying the most closely related lineage of the query sequence.”
Aligning short reads to reference alignments and trees (2011, methodology): “For phylogenetic analysis of such metagenomic environmental samples, new likelihoodbased methods such as the Evolutionary Placement Algorithm (EPA) (Berger et al., 2011; Stark et al., 2010) and pplacer (Matsen et al., 2010) have recently become available.”
The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women (2014, methodology): “1.alpha08 [236]. pplacer makes taxonomic assignment using a linear time maximum-likelihood method (or alternatively a Bayesian phylogenetic placement method) using a community specific reference tree.”
Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood (2011, neutral): “A comparative study is included in Matsen et al. (2010).”
ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data (2017, background): “…et al. 2014), EPA (Berger, Krompass & Stamatakis 2011), HYPHY (Pond, Frost & Muse 2005), PAML (Yang 2007), PHYLODOG (Bastien et al. 2013) , PPLACER (Matsen, Kodner & Armbrust 2010), RAXML (Stamatakis 2014), REVBAYES (Sebastian et al. 2014) and R 8 S (Sanderson 2003) (Table 1) can also be parsed…”
Is the distribution of Prochlorococcus and Synechococcus ecotypes in the Mediterranean Sea affected by global warming (2011, background): “0, which places sequences into a reference tree (Matsen et al., 2010).”