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| @article{parks.2018.natbiotechnol, | ||
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| title = {{TreeCluster}: {Clustering} biological sequences using phylogenetic trees}, | ||
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| urldate = {2024-08-14}, | ||
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| @book{sokal.1995, | ||
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| @article{schneider.1990.nucleicacidsres, | ||
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| @article{widmann.2006.molcellproteomics, | ||
| author = {Widmann, Jeremy and Hamady, Micah and Knight, Rob}, | ||
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| pages = {1520--1532}, | ||
| title = {{DivergentSet}, a tool for picking non-redundant sequences from large sequence collections.}, | ||
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| @article{lake.1994.procnatlacadsciua, | ||
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| journal = {Proc Natl Acad Sci U S A}, | ||
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| volume = {52}, | ||
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| @inproceedings{numba, | ||
| address = {New York, NY, USA}, | ||
| author = {Lam, Siu Kwan and Pitrou, Antoine and Seibert, Stanley}, | ||
| booktitle = {Proceedings of the {Second} {Workshop} on the {LLVM} {Compiler} {Infrastructure} in {HPC}}, | ||
| month = nov, | ||
| pages = {1--6}, | ||
| publisher = {Association for Computing Machinery}, | ||
| series = {{LLVM} '15}, | ||
| title = {Numba: a {LLVM}-based {Python} {JIT} compiler}, | ||
| year = {2015}} | ||
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| @article{zhu.2019.nat.commun, | ||
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| doi = {10.1038/s41467-019-13443-4}, | ||
| journal = {Nature Communications}, | ||
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| pages = {5477}, | ||
| pmid = {31792218}, | ||
| title = {Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains {Bacteria} and {Archaea}}, | ||
| url = {https://doi.org/10.1038/s41467-019-13443-4}, | ||
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| @book{sokal.1995, | ||
| address = {New York}, | ||
| author = {Sokal, R R and Rohlf, F J}, | ||
| edition = {3}, | ||
| publisher = {W. H. Freeman and Company}, | ||
| title = {Biometry}, | ||
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| @article{knight.2007.genomebiol, | ||
| author = {Knight, R and Maxwell, P and Birmingham, A and Carnes, J and Caporaso, J G and Easton, B C and Eaton, M and Hamady, M and Lindsay, H and Liu, Z and Lozupone, C and McDonald, D and Robeson, M and Sammut, R and Smit, S and Wakefield, M J and Widmann, J and Wikman, S and Wilson, S and Ying, H and Huttley, G A}, | ||
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| @article{lake.1994.procnatlacadsciua, | ||
| author = {Lake, J A}, | ||
| journal = {Proc Natl Acad Sci U S A}, | ||
| number = {4}, | ||
| pages = {1455--1459}, | ||
| title = {Reconstructing evolutionary trees from {DNA} and protein sequences: paralinear distances.}, | ||
| volume = {91}, | ||
| year = {1994}} | ||
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| @article{cleveland.1979.j.am.stat.assoc, | ||
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| doi = {10.1080/01621459.1979.10481038}, | ||
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| urldate = {2024-08-26}, | ||
| volume = {74}, | ||
| year = {1979}} | ||
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| @article{schneider.1990.nucleicacidsres, | ||
| author = {Schneider, T D and Stephens, R M}, | ||
| journal = {Nucleic acids research}, | ||
| month = oct, | ||
| number = {20}, | ||
| pages = {6097--100}, | ||
| title = {Sequence logos: a new way to display consensus sequences.}, | ||
| volume = {18}, | ||
| year = {1990}} | ||
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| @article{ondov.2016.mash, | ||
| title={Mash: fast genome and metagenome distance estimation using MinHash}, | ||
| author={Ondov, Brian D and Treangen, Todd J and Melsted, P{\'a}ll and Mallonee, Adam B and Bergman, Nicholas H and Koren, Sergey and Phillippy, Adam M}, | ||
| journal={Genome biology}, | ||
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| title={IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era}, | ||
| author={Minh, Bui Quang and Schmidt, Heiko A and Chernomor, Olga and Schrempf, Dominik and Woodhams, Michael D and Von Haeseler, Arndt and Lanfear, Robert}, | ||
| journal={Molecular biology and evolution}, | ||
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| year={2020}, | ||
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| } | ||
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| @article{murtagh.2012.algorithms, | ||
| title={Algorithms for hierarchical clustering: an overview}, | ||
| author={Murtagh, Fionn and Contreras, Pedro}, | ||
| journal={Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery}, | ||
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| pages={86--97}, | ||
| year={2012}, | ||
| publisher={Wiley Online Library} | ||
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||
| @article{tavare.1986.some, | ||
| title={Some probabilistic and statistical problems on the analysis of DNA sequence.}, | ||
| author={Tavar{\'e}, Simon}, | ||
| journal={Lecture of Mathematics for Life Science}, | ||
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| pages={57}, | ||
| year={1986} | ||
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| @article{saitou.1987.mol.biol.evol, | ||
| author = {Saitou, N and Nei, M}, | ||
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| pages = {406--425}, | ||
| title = {The neighbor-joining method: a new method for reconstructing phylogenetic trees}, | ||
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| year = {1987}} | ||
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| @article{saitou.1987.mol.biol.evol, | ||
| author = {Saitou, N and Nei, M}, | ||
| journal = {Mol. Biol. Evol.}, | ||
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| pages = {406--425}, | ||
| title = {The neighbor-joining method: a new method for reconstructing phylogenetic trees}, | ||
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| year = {1987}} | ||
| @article{parks.2018.natbiotechnol, | ||
| author = {Parks, Donovan H. and Chuvochina, Maria and Waite, David W. and Rinke, Christian and Skarshewski, Adam and Chaumeil, Pierre-Alain and Hugenholtz, Philip}, | ||
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| @article{balaban.2019.plosone, | ||
| author = {Balaban, Metin and Moshiri, Niema and Mai, Uyen and Jia, Xingfan and Mirarab, Siavash}, | ||
| journal = {PLOS ONE}, | ||
| month = aug, | ||
| number = {8}, | ||
| pages = {e0221068}, | ||
| title = {{TreeCluster}: {Clustering} biological sequences using phylogenetic trees}, | ||
| volume = {14}, | ||
| year = {2019}} | ||
| @inproceedings{numba, | ||
| address = {New York, NY, USA}, | ||
| author = {Lam, Siu Kwan and Pitrou, Antoine and Seibert, Stanley}, | ||
| booktitle = {Proceedings of the {Second} {Workshop} on the {LLVM} {Compiler} {Infrastructure} in {HPC}}, | ||
| doi = {10.1145/2833157.2833162}, | ||
| isbn = {978-1-4503-4005-2}, | ||
| month = nov, | ||
| pages = {1--6}, | ||
| publisher = {Association for Computing Machinery}, | ||
| series = {{LLVM} '15}, | ||
| shorttitle = {Numba}, | ||
| title = {Numba: a {LLVM}-based {Python} {JIT} compiler}, | ||
| url = {https://dl.acm.org/doi/10.1145/2833157.2833162}, | ||
| urldate = {2024-09-22}, | ||
| year = {2015}} | ||
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||
| @article{minh.2020.iq, | ||
| author = {Minh, Bui Quang and Schmidt, Heiko A and Chernomor, Olga and Schrempf, Dominik and Woodhams, Michael D and von Haeseler, Arndt and Lanfear, Robert}, | ||
| doi = {10.1093/molbev/msaa015}, | ||
| issn = {0737-4038}, | ||
| journal = {Molecular Biology and Evolution}, | ||
| month = may, | ||
| number = {5}, | ||
| pages = {1530--1534}, | ||
| shorttitle = {{IQ}-{TREE} 2}, | ||
| title = {{IQ}-{TREE} 2: {New} {Models} and {Efficient} {Methods} for {Phylogenetic} {Inference} in the {Genomic} {Era}}, | ||
| url = {https://doi.org/10.1093/molbev/msaa015}, | ||
| urldate = {2024-10-16}, | ||
| volume = {37}, | ||
| year = {2020}} | ||
|
|
||
| @article{murtagh.2012.algorithms, | ||
| author = {Murtagh, Fionn and Contreras, Pedro}, | ||
| doi = {10.1002/widm.53}, | ||
| issn = {1942-4795}, | ||
| journal = {WIREs Data Mining and Knowledge Discovery}, | ||
| language = {en}, | ||
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| pages = {86--97}, | ||
| shorttitle = {Algorithms for hierarchical clustering}, | ||
| title = {Algorithms for hierarchical clustering: an overview}, | ||
| url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/widm.53}, | ||
| urldate = {2025-01-12}, | ||
| volume = {2}, | ||
| year = {2012}} | ||
|
|
||
| @article{ondov.2016.mash, | ||
| author = {Ondov, Brian D. and Treangen, Todd J. and Melsted, P?ll and Mallonee, Adam B. and Bergman, Nicholas H. and Koren, Sergey and Phillippy, Adam M.}, | ||
| doi = {10.1186/s13059-016-0997-x}, | ||
| issn = {1474-760X}, | ||
| journal = {Genome Biology}, | ||
| month = dec, | ||
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| pages = {132}, | ||
| title = {Mash: fast genome and metagenome distance estimation using {MinHash}}, | ||
| url = {http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x}, | ||
| urldate = {2017-07-04}, | ||
| volume = {17}, | ||
| year = {2016}} | ||
|
|
||
| @article{tavare.1986.some, | ||
| author = {Tavare, S}, | ||
| journal = {Lec. Math. Life Sci.}, | ||
| pages = {57--86}, | ||
| title = {Some probabilistic and statistical problems in the analysis of {DNA} sequences.}, | ||
| volume = {17}, | ||
| year = {1986}} |