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@article{SEPP,
title={Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information},
author={Janssen, Stefan and McDonald, Daniel and Gonzalez, Antonio and Navas-Molina, Jose A. and Jiang, Lingjing and Xu, Zhenjiang Zech and Winker, Kevin and Kado, Deborah M. and Orwoll, Eric and Manary, Mark and Mirarab, Siavash and Knight, Rob},
journal={mSystems},
volume={3},
number={3},
year={2018},
publisher={American Society for Microbiology Journals},
doi={10.1128/mSystems.00021-18},
}
@article{10.1371/journal.pone.0031009,
author = {Matsen, Frederick A. AND Hoffman, Noah G. AND Gallagher, Aaron AND Stamatakis, Alexandros},
journal = {PLOS ONE},
publisher = {Public Library of Science},
title = {A Format for Phylogenetic Placements},
year = {2012},
month = {02},
volume = {7},
url = {https://doi.org/10.1371/journal.pone.0031009},
pages = {1-4},
abstract = {We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g., short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them. The format is lightweight, versatile, extensible, and is based on the JSON format, which can be parsed by most modern programming languages. Our format is already implemented in several tools for computing and post-processing parsimony- and likelihood-based phylogenetic placements and has worked well in practice. We believe that establishing a standard format for analyzing read placements at this early stage will lead to a more efficient development of powerful and portable post-analysis tools for the growing applications of phylogenetic placement.},
number = {2},
doi = {10.1371/journal.pone.0031009}
}
@article{hmmer,
author={Eddy, Sean R.},
journal={PLOS Computational Biology},
publisher={Public Library of Science},
title={Accelerated Profile HMM Searches},
year={2011},
month={10},
volume={7},
url={https://doi.org/10.1371/journal.pcbi.1002195},
pages={1-16},
number={10},
doi={10.1371/journal.pcbi.1002195}
}
@article{pplacer,
title={pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree},
author={Matsen, Frederick A and Kodner, Robin B and Armbrust, E Virginia},
journal={BMC bioinformatics},
volume={11},
number={1},
pages={538},
year={2010},
publisher={BioMed Central}
}
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