packages.bib

@Manual{R-ape,
  title = {ape: Analyses of Phylogenetics and Evolution},
  author = {Emmanuel Paradis and Simon Blomberg and Ben Bolker and Joseph Brown and Santiago Claramunt and Julien Claude and Hoa Sien Cuong and Richard Desper and Gilles Didier and Benoit Durand and Julien Dutheil and RJ Ewing and Olivier Gascuel and Thomas Guillerme and Christoph Heibl and Anthony Ives and Bradley Jones and Franz Krah and Daniel Lawson and Vincent Lefort and Pierre Legendre and Jim Lemon and Guillaume Louvel and Eric Marcon and Rosemary McCloskey and Johan Nylander and Rainer Opgen-Rhein and Andrei-Alin Popescu and Manuela Royer-Carenzi and Klaus Schliep and Korbinian Strimmer and Damien {de Vienne}},
  year = {2020},
  note = {R package version 5.4},
  url = {https://CRAN.R-project.org/package=ape},
}
@Manual{R-base,
  title = {R: A Language and Environment for Statistical Computing},
  author = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2019},
  url = {https://www.R-project.org/},
}
@Manual{R-bookdown,
  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
  author = {Yihui Xie},
  year = {2020},
  note = {R package version 0.19},
  url = {https://CRAN.R-project.org/package=bookdown},
}
@Manual{R-broom.mixed,
  title = {broom.mixed: Tidying Methods for Mixed Models},
  author = {Ben Bolker and David Robinson},
  year = {2020},
  note = {R package version 0.2.6},
  url = {https://CRAN.R-project.org/package=broom.mixed},
}
@Manual{R-data.table,
  title = {data.table: Extension of `data.frame`},
  author = {Matt Dowle and Arun Srinivasan},
  year = {2019},
  note = {R package version 1.12.8},
  url = {https://CRAN.R-project.org/package=data.table},
}
@Manual{R-dplyr,
  title = {dplyr: A Grammar of Data Manipulation},
  author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller},
  year = {2020},
  note = {R package version 1.0.0},
  url = {https://CRAN.R-project.org/package=dplyr},
}
@Manual{R-forcats,
  title = {forcats: Tools for Working with Categorical Variables (Factors)},
  author = {Hadley Wickham},
  year = {2020},
  note = {R package version 0.5.0},
  url = {https://CRAN.R-project.org/package=forcats},
}
@Manual{R-geiger,
  title = {geiger: Analysis of Evolutionary Diversification},
  author = {Luke Harmon and Matthew Pennell and Chad Brock and Joseph Brown and Wendell Challenger and Jon Eastman and Rich FitzJohn and Rich Glor and Gene Hunt and Liam Revell and Graham Slater and Josef Uyeda and Jason Weir},
  year = {2020},
  note = {R package version 2.0.7},
  url = {https://CRAN.R-project.org/package=geiger},
}
@Manual{R-gghighlight,
  title = {gghighlight: Highlight Lines and Points in 'ggplot2'},
  author = {Hiroaki Yutani},
  year = {2020},
  note = {R package version 0.3.0},
  url = {https://CRAN.R-project.org/package=gghighlight},
}
@Manual{R-ggimage,
  title = {ggimage: Use Image in 'ggplot2'},
  author = {Guangchuang Yu},
  year = {2020},
  note = {R package version 0.2.8},
  url = {https://CRAN.R-project.org/package=ggimage},
}
@Manual{R-ggnewscale,
  title = {ggnewscale: Multiple Fill and Colour Scales in 'ggplot2'},
  author = {Elio Campitelli},
  year = {2020},
  note = {R package version 0.4.1},
  url = {https://CRAN.R-project.org/package=ggnewscale},
}
@Manual{R-ggplot2,
  title = {ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics},
  author = {Hadley Wickham and Winston Chang and Lionel Henry and Thomas Lin Pedersen and Kohske Takahashi and Claus Wilke and Kara Woo and Hiroaki Yutani and Dewey Dunnington},
  year = {2020},
  note = {R package version 3.3.2},
  url = {https://CRAN.R-project.org/package=ggplot2},
}
@Manual{R-ggplotify,
  title = {ggplotify: Convert Plot to 'grob' or 'ggplot' Object},
  author = {Guangchuang Yu},
  year = {2020},
  note = {R package version 0.0.5},
  url = {https://CRAN.R-project.org/package=ggplotify},
}
@Manual{R-ggpubr,
  title = {ggpubr: 'ggplot2' Based Publication Ready Plots},
  author = {Alboukadel Kassambara},
  year = {2020},
  note = {R package version 0.3.0},
  url = {https://CRAN.R-project.org/package=ggpubr},
}
@Manual{R-ggrepel,
  title = {ggrepel: Automatically Position Non-Overlapping Text Labels with
'ggplot2'},
  author = {Kamil Slowikowski},
  year = {2020},
  note = {R package version 0.8.2},
  url = {https://CRAN.R-project.org/package=ggrepel},
}
@Manual{R-ggsci,
  title = {ggsci: Scientific Journal and Sci-Fi Themed Color Palettes for
'ggplot2'},
  author = {Nan Xiao},
  year = {2018},
  note = {R package version 2.9},
  url = {https://CRAN.R-project.org/package=ggsci},
}
@Manual{R-ggtree,
  title = {ggtree: an R package for visualization of tree and annotation data},
  author = {Guangchuang Yu and Tommy Tsan-Yuk Lam},
  year = {2020},
  note = {R package version 2.3.1},
  url = {https://yulab-smu.github.io/treedata-book/},
}
@Manual{R-kableExtra,
  title = {kableExtra: Construct Complex Table with 'kable' and Pipe Syntax},
  author = {Hao Zhu},
  year = {2019},
  note = {R package version 1.1.0},
  url = {https://CRAN.R-project.org/package=kableExtra},
}
@Manual{R-magick,
  title = {magick: Advanced Graphics and Image-Processing in R},
  author = {Jeroen Ooms},
  year = {2020},
  note = {R package version 2.4.0},
  url = {https://CRAN.R-project.org/package=magick},
}
@Manual{R-magrittr,
  title = {magrittr: A Forward-Pipe Operator for R},
  author = {Stefan Milton Bache and Hadley Wickham},
  year = {2014},
  note = {R package version 1.5},
  url = {https://CRAN.R-project.org/package=magrittr},
}
@Manual{R-nlme,
  title = {nlme: Linear and Nonlinear Mixed Effects Models},
  author = {José Pinheiro and Douglas Bates and {R-core}},
  year = {2020},
  note = {R package version 3.1-148},
  url = {https://CRAN.R-project.org/package=nlme},
}
@Manual{R-plotly,
  title = {plotly: Create Interactive Web Graphics via 'plotly.js'},
  author = {Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and Marianne Corvellec and Pedro Despouy},
  year = {2020},
  note = {R package version 4.9.2.1},
  url = {https://CRAN.R-project.org/package=plotly},
}
@Manual{R-purrr,
  title = {purrr: Functional Programming Tools},
  author = {Lionel Henry and Hadley Wickham},
  year = {2020},
  note = {R package version 0.3.4},
  url = {https://CRAN.R-project.org/package=purrr},
}
@Manual{R-readr,
  title = {readr: Read Rectangular Text Data},
  author = {Hadley Wickham and Jim Hester and Romain Francois},
  year = {2018},
  note = {R package version 1.3.1},
  url = {https://CRAN.R-project.org/package=readr},
}
@Manual{R-stargazer,
  title = {stargazer: Well-Formatted Regression and Summary Statistics Tables},
  author = {Marek Hlavac},
  year = {2018},
  note = {R package version 5.2.2},
  url = {https://CRAN.R-project.org/package=stargazer},
}
@Manual{R-stringr,
  title = {stringr: Simple, Consistent Wrappers for Common String Operations},
  author = {Hadley Wickham},
  year = {2019},
  note = {R package version 1.4.0},
  url = {https://CRAN.R-project.org/package=stringr},
}
@Manual{R-tibble,
  title = {tibble: Simple Data Frames},
  author = {Kirill Müller and Hadley Wickham},
  year = {2020},
  note = {R package version 3.0.1},
  url = {https://CRAN.R-project.org/package=tibble},
}
@Manual{R-tidyr,
  title = {tidyr: Tidy Messy Data},
  author = {Hadley Wickham and Lionel Henry},
  year = {2020},
  note = {R package version 1.1.0},
  url = {https://CRAN.R-project.org/package=tidyr},
}
@Manual{R-tidytree,
  title = {tidytree: A Tidy Tool for Phylogenetic Tree Data Manipulation},
  author = {Guangchuang Yu},
  year = {2020},
  note = {R package version 0.3.3.991},
  url = {https://yulab-smu.github.io/treedata-book/},
}
@Manual{R-tidyverse,
  title = {tidyverse: Easily Install and Load the 'Tidyverse'},
  author = {Hadley Wickham},
  year = {2019},
  note = {R package version 1.3.0},
  url = {https://CRAN.R-project.org/package=tidyverse},
}
@Manual{R-treeio,
  title = {treeio: Base Classes and Functions for Phylogenetic Tree Input and
Output},
  author = {Guangchuang Yu},
  year = {2020},
  note = {https://github.com/YuLab-SMU/treeio (devel),
https://docs.ropensci.org/treeio/ (docs),
https://yulab-smu.github.io/treedata-book/ (book)},
}
@Manual{R-UpSetR,
  title = {UpSetR: A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting Sets},
  author = {Nils Gehlenborg},
  year = {2019},
  note = {R package version 1.4.0},
  url = {https://CRAN.R-project.org/package=UpSetR},
}
@Article{ape2019,
  title = {ape 5.0: an environment for modern phylogenetics and evolutionary analyses in {R}},
  author = {E. Paradis and K. Schliep},
  journal = {Bioinformatics},
  year = {2019},
  volume = {35},
  pages = {526-528},
}
@Book{bookdown2016,
  title = {bookdown: Authoring Books and Technical Documents with {R} Markdown},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2016},
  note = {ISBN 978-1138700109},
  url = {https://github.com/rstudio/bookdown},
}
@Article{geiger2009,
  title = {Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates},
  author = {ME Alfaro and F Santini and C Brock and H Alamillo and A Dornburg and DL Rabosky and G Carnevale and LJ Harmon},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  year = {2009},
  volume = {106},
  pages = {13410-13414},
}
@Article{geiger2011,
  title = {A novel comparative method for identifying shifts in the rate of character evolution on trees},
  author = {JM Eastman and ME Alfaro and P Joyce and AL Hipp and LJ Harmon},
  journal = {Evolution},
  year = {2011},
  volume = {65},
  pages = {3578-3589},
}
@Article{geiger2012,
  title = {Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation},
  author = {GJ Slater and LJ Harmon and D Wegmann and P Joyce and LJ Revell and ME Alfaro},
  journal = {Evolution},
  year = {2012},
  volume = {66},
  pages = {752-762},
}
@Article{geiger2008,
  title = {GEIGER: investigating evolutionary radiations},
  author = {LJ Harmon and JT Weir and CD Brock and RE Glor and W Challenger},
  journal = {Bioinformatics},
  year = {2008},
  volume = {24},
  pages = {129-131},
}
@Article{geiger2014,
  title = {geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees},
  author = {MW Pennell and JM Eastman and GJ Slater and JW Brown and JC Uyeda and RG Fitzjohn and ME Alfaro and LJ Harmon},
  journal = {Bioinformatics},
  year = {2014},
  volume = {30},
  pages = {2216-2218},
}
@Book{ggplot22016,
  author = {Hadley Wickham},
  title = {ggplot2: Elegant Graphics for Data Analysis},
  publisher = {Springer-Verlag New York},
  year = {2016},
  isbn = {978-3-319-24277-4},
  url = {https://ggplot2.tidyverse.org},
}
@Article{ggtree2020,
  title = {Using ggtree to Visualize Data on Tree-Like Structures},
  author = {Guangchuang Yu},
  year = {2020},
  journal = {Current Protocols in Bioinformatics},
  volume = {69},
  pages = {e96},
  number = {1},
  url = {https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpbi.96},
  doi = {10.1002/cpbi.96},
}
@Article{ggtree2018,
  title = {Two methods for mapping and visualizing associated data on phylogeny using ggtree.},
  author = {Guangchuang Yu and Tommy Tsan-Yuk Lam and Huachen Zhu and Yi Guan},
  year = {2018},
  journal = {Molecular Biology and Evolution},
  volume = {35},
  issue = {2},
  pages = {3041-3043},
  doi = {10.1093/molbev/msy194},
  url = {https://academic.oup.com/mbe/article/35/12/3041/5142656},
}
@Article{ggtree2017,
  title = {ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.},
  author = {Guangchuang Yu and David Smith and Huachen Zhu and Yi Guan and Tommy Tsan-Yuk Lam},
  year = {2017},
  journal = {Methods in Ecology and Evolution},
  volume = {8},
  issue = {1},
  pages = {28-36},
  doi = {10.1111/2041-210X.12628},
  url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract},
}
@Book{plotly2020,
  author = {Carson Sievert},
  title = {Interactive Web-Based Data Visualization with R, plotly, and shiny},
  publisher = {Chapman and Hall/CRC},
  year = {2020},
  isbn = {9781138331457},
  url = {https://plotly-r.com},
}
@Article{tidyverse2019,
  title = {Welcome to the {tidyverse}},
  author = {Hadley Wickham and Mara Averick and Jennifer Bryan and Winston Chang and Lucy D'Agostino McGowan and Romain François and Garrett Grolemund and Alex Hayes and Lionel Henry and Jim Hester and Max Kuhn and Thomas Lin Pedersen and Evan Miller and Stephan Milton Bache and Kirill Müller and Jeroen Ooms and David Robinson and Dana Paige Seidel and Vitalie Spinu and Kohske Takahashi and Davis Vaughan and Claus Wilke and Kara Woo and Hiroaki Yutani},
  year = {2019},
  journal = {Journal of Open Source Software},
  volume = {4},
  number = {43},
  pages = {1686},
  doi = {10.21105/joss.01686},
}
@Article{treeio2020,
  title = {treeio: an R package for phylogenetic tree input and output with richly annotated and associated data.},
  author = {Li-Gen Wang and Tommy Tsan-Yuk Lam and Shuangbin Xu and Zehan Dai and Lang Zhou and Tingze Feng and Pingfan Guo and Casey W. Dunn and Bradley R. Jones and Tyler Bradley and Huachen Zhu and Yi Guan and Yong Jiang and Guangchuang Yu},
  year = {2020},
  journal = {Molecular Biology and Evolution},
  volume = {37},
  issue = {2},
  pages = {599-603},
  doi = {10.1093/molbev/msz240},
}
@book{python3,
 author = {Van Rossum, Guido and Drake, Fred L.},
 title = {Python 3 Reference Manual},
 year = {2009},
 isbn = {1441412697},
 publisher = {CreateSpace},
 address = {Scotts Valley, CA}
}
@article{Biopython,
    author = {Cock, Peter J. A. and Antao, Tiago and Chang, Jeffrey T. and Chapman, Brad A. and Cox, Cymon J. and Dalke, Andrew and Friedberg, Iddo and Hamelryck, Thomas and Kauff, Frank and Wilczynski, Bartek and de Hoon, Michiel J. L.},
    title = "{Biopython: freely available Python tools for computational molecular biology and bioinformatics}",
    journal = {Bioinformatics},
    volume = {25},
    number = {11},
    pages = {1422-1423},
    year = {2009},
    month = {03},
    abstract = "{Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning.Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license.Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/\_Mailing\_listspeter.cock@scri.ac.uk.}",
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btp163},
    url = {https://doi.org/10.1093/bioinformatics/btp163},
    eprint = {https://academic.oup.com/bioinformatics/article-pdf/25/11/1422/944180/btp163.pdf},
}
@article{snakemake,
    author = {Köster, Johannes and Rahmann, Sven},
    title = "{Snakemake - a scalable bioinformatics workflow engine}",
    journal = {Bioinformatics},
    volume = {28},
    number = {19},
    pages = {2520-2522},
    year = {2012},
    month = {08},
    abstract = "{Summary: Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow. It is the first system to support the use of automatically inferred multiple named wildcards (or variables) in input and output filenames.Availability:http://snakemake.googlecode.com.Contact:johannes.koester@uni-due.de}",
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/bts480},
    url = {https://doi.org/10.1093/bioinformatics/bts480},
    eprint = {https://academic.oup.com/bioinformatics/article-pdf/28/19/2520/819790/bts480.pdf},
}
@misc{dill,
    title={Building a Framework for Predictive Science},
    author={Michael M. McKerns and Leif Strand and Tim Sullivan and Alta Fang and Michael A. G. Aivazis},
    year={2012},
    eprint={1202.1056},
    archivePrefix={arXiv},
    primaryClass={cs.MS}
}
@InProceedings{ mckinney-proc-scipy-2010,
  author    = { {W}es {M}c{K}inney },
  title     = { {D}ata {S}tructures for {S}tatistical {C}omputing in {P}ython },
  booktitle = { {P}roceedings of the 9th {P}ython in {S}cience {C}onference },
  pages     = { 56 - 61 },
  year      = { 2010 },
  editor    = { {S}t\'efan van der {W}alt and {J}arrod {M}illman },
  doi       = { 10.25080/Majora-92bf1922-00a }
}
@article{mygene,
  author   = {Xin, Jiwen and Mark, Adam and Afrasiabi, Cyrus and Tsueng, Ginger and Juchler, Moritz and Gopal, Nikhil and Stupp, Gregory S. and Putman, Timothy E. and Ainscough, Benjamin J. and Griffith, Obi L. and Torkamani, Ali and Whetzel, Patricia L. and Mungall, Christopher J. and Mooney, Sean D. and Su, Andrew I. and Wu, Chunlei},
  title    = {High-performance web services for querying gene and variant annotation},
  issn     = {1474-760X},
  number   = {1},
  pages    = {91},
  url      = {https://doi.org/10.1186/s13059-016-0953-9},
  volume   = {17},
  abstract = {Efficient tools for data management and integration are essential for many aspects of high-throughput biology. In particular, annotations of genes and human genetic variants are commonly used but highly fragmented across many resources. Here, we describe MyGene.info and MyVariant.info, high-performance web services for querying gene and variant annotation information. These web services are currently accessed more than three million times per month. They also demonstrate a generalizable cloud-based model for organizing and querying biological annotation information. MyGene.info and MyVariant.info are provided as high-performance web services, accessible at http://mygene.infoand http://myvariant.info. Both are offered free of charge to the research community.},
  journal  = {Genome Biology},
  refid    = {Xin2016},
  year     = {2016},
}
@software{pandas,
  author       = {Jeff Reback and
                  Wes McKinney and
                  jbrockmendel and
                  Joris Van den Bossche and
                  Tom Augspurger and
                  Phillip Cloud and
                  gfyoung and
                  Sinhrks and
                  Adam Klein and
                  Simon Hawkins and
                  Matthew Roeschke and
                  Jeff Tratner and
                  Chang She and
                  William Ayd and
                  Terji Petersen and
                  MomIsBestFriend and
                  Marc Garcia and
                  Jeremy Schendel and
                  Andy Hayden and
                  Vytautas Jancauskas and
                  Pietro Battiston and
                  Daniel Saxton and
                  Skipper Seabold and
                  alimcmaster1 and
                  chris-b1 and
                  h-vetinari and
                  Stephan Hoyer and
                  Kaiqi Dong and
                  Wouter Overmeire and
                  Martin Winkel},
  title        = {pandas-dev/pandas: Pandas 1.0.5},
  month        = jun,
  year         = 2020,
  publisher    = {Zenodo},
  version      = {v1.0.5},
  doi          = {10.5281/zenodo.3898987},
  url          = {https://doi.org/10.5281/zenodo.3898987}
}
@Article{bioconda,
  author  = {Grüning, Björn and Dale, Ryan and Sjödin, Andreas and Chapman, Brad A. and Rowe, Jillian and Tomkins-Tinch, Christopher H. and Valieris, Renan and Köster, Johannes and Team, The Bioconda},
  title   = {Bioconda: sustainable and comprehensive software distribution for the life sciences},
  issn    = {1548-7105},
  number  = {7},
  pages   = {475--476},
  url     = {https://doi.org/10.1038/s41592-018-0046-7},
  volume  = {15},
  journal = {Nature Methods},
  refid   = {Grüning2018},
  year    = {2018},
}