Rough in content with citations

joss/paper.bib

@@ -1,3 +1,30 @@
+@article{blancomiguez2023extending,
+  title = {Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4},
+  author = {Blanco-Míguez,  Aitor and Beghini,  Francesco and Cumbo,  Fabio and McIver,  Lauren J. and Thompson,  Kelsey N. and Zolfo,  Moreno and Manghi,  Paolo and Dubois,  Leonard and Huang,  Kun D. and Thomas,  Andrew Maltez and Nickols,  William A. and Piccinno,  Gianmarco and Piperni,  Elisa and Punčochář,  Michal and Valles-Colomer,  Mireia and Tett,  Adrian and Giordano,  Francesca and Davies,  Richard and Wolf,  Jonathan and Berry,  Sarah E. and Spector,  Tim D. and Franzosa,  Eric A. and Pasolli,  Edoardo and Asnicar,  Francesco and Huttenhower,  Curtis and Segata,  Nicola},
+  year = 2023,
+  month = feb,
+  journal = {Nature Biotechnology},
+  publisher = {Springer Science and Business Media LLC},
+  volume = 41,
+  number = 11,
+  pages = {1633--1644},
+  doi = {10.1038/s41587-023-01688-w},
+  issn = {1546-1696},
+  url = {http://dx.doi.org/10.1038/s41587-023-01688-w},
+}
+@article{boickaert2014beast,
+  title = {BEAST 2: A Software Platform for Bayesian Evolutionary Analysis},
+  author = {Bouckaert, Remco AND Heled, Joseph AND Kühnert, Denise AND Vaughan, Tim AND Wu, Chieh-Hsi AND Xie, Dong AND Suchard, Marc A. AND Rambaut, Andrew AND Drummond, Alexei J.},
+  year = 2014,
+  month = {04},
+  journal = {PLOS Computational Biology},
+  publisher = {Public Library of Science},
+  volume = 10,
+  number = 4,
+  pages = {1--6},
+  doi = {10.1371/journal.pcbi.1003537},
+  url = {https://doi.org/10.1371/journal.pcbi.1003537},
+}
 @article{challa2019phylogenetic,
   title = {Phylogenetic trees: applications, construction, and assessment},
   author = {Challa, Surekha and Neelapu, Nageswara Rao Reddy},
@@ -7,7 +34,29 @@ @article{challa2019phylogenetic
   pages = {167--192},
   doi = {10.1007/978-3-030-19318-8_10},
 }
-
+@article{cock2009biopython,
+  title = {Biopython: freely available Python tools for computational molecular biology and bioinformatics},
+  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.},
+  year = 2009,
+  month = {03},
+  journal = {Bioinformatics},
+  volume = 25,
+  number = 11,
+  pages = {1422--1423},
+  doi = {10.1093/bioinformatics/btp163},
+  issn = {1367-4803},
+  url = {https://doi.org/10.1093/bioinformatics/btp163},
+  eprint = {https://academic.oup.com/bioinformatics/article-pdf/25/11/1422/48989335/bioinformatics\_25\_11\_1422.pdf},
+}
+@misc{dolson2024phylotrack,
+  title = {Phylotrack: C++ and Python libraries for in silico phylogenetic tracking},
+  author = {Dolson,  Emily and Rodriguez-Papa,  Santiago and Moreno,  Matthew Andres},
+  year = 2024,
+  publisher = {arXiv},
+  doi = {10.48550/arxiv.2405.09389},
+  url = {https://arxiv.org/abs/2405.09389},
+  copyright = {arXiv.org perpetual,  non-exclusive license},
+}
 @article{emerson2008phylogenetic,
   title = {Phylogenetic analysis of community assembly and structure over space and time},
   author = {Emerson, Brent C. and Gillespie, Rosemary G.},
@@ -19,19 +68,6 @@ @article{emerson2008phylogenetic
   pages = {619--630},
   doi = {10.1016/j.tree.2008.07.005},
 }
-
-@article{mirSoundCollesslikeBalance2018,
-  title = {Sound Colless-like balance indices for multifurcating trees},
-  author = {Mir, Arnau and Rotger, Lucía and Rosselló, Francesc},
-  volume = 13,
-  number = 9,
-  pages = {e0203401},
-  doi = {10.1371/journal.pone.0203401},
-  journaltitle = {{Plos} {One}},
-  shortjournal = {{Plos} {One}},
-  date = {2018-09-25},
-}
-
 @article{faithConservationEvaluationPhylogenetic1992,
   title = {Conservation evaluation and phylogenetic diversity},
   author = {Faith, Daniel P.},
@@ -43,15 +79,274 @@ @article{faithConservationEvaluationPhylogenetic1992
   shortjournal = {Biological Conservation},
   date = {1992-01-01},
 }
-
+@article{felsenstein1981evolutionary,
+  title = {Evolutionary trees from DNA sequences: A maximum likelihood approach},
+  author = {Felsenstein,  Joseph},
+  year = 1981,
+  month = nov,
+  journal = {Journal of Molecular Evolution},
+  publisher = {Springer Science and Business Media LLC},
+  volume = 17,
+  number = 6,
+  pages = {368--376},
+  doi = {10.1007/bf01734359},
+  issn = {1432-1432},
+  url = {http://dx.doi.org/10.1007/BF01734359},
+}
+@article{huertacepas2016ete,
+  title = {ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data},
+  author = {Huerta-Cepas, Jaime and Serra, François and Bork, Peer},
+  year = 2016,
+  month = {02},
+  journal = {Molecular Biology and Evolution},
+  volume = 33,
+  number = 6,
+  pages = {1635--1638},
+  doi = {10.1093/molbev/msw046},
+  issn = {0737-4038},
+  url = {https://doi.org/10.1093/molbev/msw046},
+  eprint = {https://academic.oup.com/mbe/article-pdf/33/6/1635/7953632/msw046.pdf},
+}
+@article{kelleher2018efficient,
+  title = {Efficient pedigree recording for fast population genetics simulation},
+  author = {Kelleher,  Jerome and Thornton,  Kevin R. and Ashander,  Jaime and Ralph,  Peter L.},
+  year = 2018,
+  month = nov,
+  journal = {PLOS Computational Biology},
+  publisher = {Public Library of Science (PLoS)},
+  volume = 14,
+  number = 11,
+  pages = {e1006581},
+  doi = {10.1371/journal.pcbi.1006581},
+  issn = {1553-7358},
+  url = {http://dx.doi.org/10.1371/journal.pcbi.1006581},
+  editor = {Kosakovsky Pond,  Sergei L.},
+}
+@article{knight2007pycogent,
+  title = {PyCogent: a toolkit for making sense from sequence},
+  author = {Knight,  Rob and Maxwell,  Peter and Birmingham,  Amanda and Carnes,  Jason and Caporaso,  J Gregory and Easton,  Brett C and Eaton,  Michael and Hamady,  Micah and Lindsay,  Helen and Liu,  Zongzhi and Lozupone,  Catherine and McDonald,  Daniel and Robeson,  Michael and Sammut,  Raymond and Smit,  Sandra and Wakefield,  Matthew J and Widmann,  Jeremy and Wikman,  Shandy and Wilson,  Stephanie and Ying,  Hua and Huttley,  Gavin A},
+  year = 2007,
+  journal = {Genome Biology},
+  publisher = {Springer Science and Business Media LLC},
+  volume = 8,
+  number = 8,
+  pages = {R171},
+  doi = {10.1186/gb-2007-8-8-r171},
+  issn = {1465-6906},
+  url = {http://dx.doi.org/10.1186/gb-2007-8-8-r171},
+}
+@article{lipman1985rapid,
+  title = {Rapid and Sensitive Protein Similarity Searches},
+  author = {Lipman,  David J. and Pearson,  William R.},
+  year = 1985,
+  month = mar,
+  journal = {Science},
+  publisher = {American Association for the Advancement of Science (AAAS)},
+  volume = 227,
+  number = 4693,
+  pages = {1435--1441},
+  doi = {10.1126/science.2983426},
+  issn = {1095-9203},
+  url = {http://dx.doi.org/10.1126/science.2983426},
+}
+@article{maddison1997nexus,
+  title = {Nexus: An Extensible File Format for Systematic Information},
+  author = {Maddison,  David R. and Swofford,  David L. and Maddison,  Wayne P.},
+  year = 1997,
+  month = dec,
+  journal = {Systematic Biology},
+  publisher = {Oxford University Press (OUP)},
+  volume = 46,
+  number = 4,
+  pages = {590--621},
+  doi = {10.1093/sysbio/46.4.590},
+  issn = {1063-5157},
+  url = {http://dx.doi.org/10.1093/sysbio/46.4.590},
+  editor = {Cannatella,  David},
+}
+@inbook{mirarab2014pasta,
+  title = {PASTA: Ultra-Large Multiple Sequence Alignment},
+  author = {Mirarab,  Siavash and Nguyen,  Nam and Warnow,  Tandy},
+  year = 2014,
+  booktitle = {Research in Computational Molecular Biology},
+  publisher = {Springer International Publishing},
+  pages = {177--191},
+  doi = {10.1007/978-3-319-05269-4_15},
+  isbn = 9783319052694,
+  issn = {1611-3349},
+  url = {http://dx.doi.org/10.1007/978-3-319-05269-4_15},
+}
+@article{mirSoundCollesslikeBalance2018,
+  title = {Sound Colless-like balance indices for multifurcating trees},
+  author = {Mir, Arnau and Rotger, Lucía and Rosselló, Francesc},
+  volume = 13,
+  number = 9,
+  pages = {e0203401},
+  doi = {10.1371/journal.pone.0203401},
+  journaltitle = {{Plos} {One}},
+  shortjournal = {{Plos} {One}},
+  date = {2018-09-25},
+}
 @article{moreno2022hstrat,
   title = {hstrat: a Python Package for phylogenetic inference on distributed digital evolution populations},
-  author = {Moreno, Matthew Andres and Dolson, Emily and Ofria, Charles},
+  author = {Moreno,  Matthew Andres and Dolson,  Emily and Ofria,  Charles},
   year = 2022,
+  month = dec,
   journal = {Journal of Open Source Software},
+  publisher = {The Open Journal},
   volume = 7,
   number = 80,
   pages = 4866,
   doi = {10.21105/joss.04866},
-  url = {https://doi.org/10.21105/joss.04866},
+  issn = {2475-9066},
+  url = {http://dx.doi.org/10.21105/joss.04866},
+}
+@article{moshiri2020treeswift,
+  title = {TreeSwift: A massively scalable Python tree package},
+  author = {Moshiri,  N.},
+  year = 2020,
+  month = jan,
+  journal = {SoftwareX},
+  publisher = {Elsevier BV},
+  volume = 11,
+  pages = 100436,
+  doi = {10.1016/j.softx.2020.100436},
+  issn = {2352-7110},
+  url = {http://dx.doi.org/10.1016/j.softx.2020.100436},
+}
+@article{neches2018suchtree,
+  title = {SuchTree: Fast,  thread-safe computations with phylogenetic trees},
+  author = {Y. Neches,  Russell and Scott,  Camille},
+  year = 2018,
+  month = jul,
+  journal = {Journal of Open Source Software},
+  publisher = {The Open Journal},
+  volume = 3,
+  number = 27,
+  pages = 678,
+  doi = {10.21105/joss.00678},
+  issn = {2475-9066},
+  url = {http://dx.doi.org/10.21105/joss.00678},
+}
+@misc{olsen1990newick,
+  title = {{N}ewick's 8:45 {T}ree {F}ormat {S}tandard},
+  author = {Gary Olsen},
+  year = 1990,
+  note = {[Accessed May 19, 2024 and archived to \url{https://perma.cc/5ZMP-MZ7F}]},
+  howpublished = {\url{https://phylipweb.github.io/phylip/newick_doc.html}},
+}
+@article{paradis2019ape,
+  title = {ape 5.0: an environment for modern phylogenetics and evolutionary analyses in {R}},
+  author = {Emmanuel Paradis and Klaus Schliep},
+  year = 2019,
+  journal = {Bioinformatics},
+  volume = 35,
+  pages = {526--528},
+  doi = {10.1093/bioinformatics/bty633},
+}
+@article{rasmussen2023espalier,
+  title = {Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests},
+  author = {Rasmussen,  David A and Guo,  Fangfang},
+  year = 2023,
+  month = jul,
+  journal = {Systematic Biology},
+  publisher = {Oxford University Press (OUP)},
+  volume = 72,
+  number = 5,
+  pages = {1154--1170},
+  doi = {10.1093/sysbio/syad040},
+  issn = {1076-836x},
+  url = {http://dx.doi.org/10.1093/sysbio/syad040},
+  editor = {Gascuel,  Olivier},
+}
+@misc{rideout2024scikitbio,
+  title = {scikit-bio/scikit-bio: scikit-bio 0.6.0},
+  author = {Jai Ram Rideout,   and Greg Caporaso,   and Evan Bolyen,   and Daniel McDonald,   and Yoshiki Vázquez Baeza,   and Jorge Cañardo Alastuey,   and Anders Pitman,   and Jamie Morton,   and Jose Navas,   and Kestrel Gorlick,   and Justine Debelius,   and Zech Xu,   and llcooljohn,   and Qiyun Zhu,   and Joshua Shorenstein,   and Matt Aton,   and Laurent Luce,   and Will Van Treuren,   and charudatta-navare,   and Antonio Gonzalez,   and Colin J. Brislawn,   and Weronika Patena,   and Karen Schwarzberg,   and teravest,   and Jens Reeder,   and Igor Sfiligoi,   and shiffer1,   and nbresnick,   and Dr. K. D. Murray,   and Johannes Radinger,},
+  year = 2024,
+  publisher = {Zenodo},
+  doi = {10.5281/zenodo.593387},
+  url = {https://zenodo.org/doi/10.5281/zenodo.593387},
+  copyright = {Creative Commons Attribution 4.0 International},
+}
+@article{ronquist2012mrbayes,
+  title = {MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space},
+  author = {Ronquist,  Fredrik and Teslenko,  Maxim and van der Mark,  Paul and Ayres,  Daniel L. and Darling,  Aaron and H\"{o}hna,  Sebastian and Larget,  Bret and Liu,  Liang and Suchard,  Marc A. and Huelsenbeck,  John P.},
+  year = 2012,
+  month = feb,
+  journal = {Systematic Biology},
+  publisher = {Oxford University Press (OUP)},
+  volume = 61,
+  number = 3,
+  pages = {539--542},
+  doi = {10.1093/sysbio/sys029},
+  issn = {1063-5157},
+  url = {http://dx.doi.org/10.1093/sysbio/sys029},
+}
+@article{sanchezreyes2021physcraper,
+  title = {Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life},
+  author = {Sánchez-Reyes,  Luna L. and Kandziora,  Martha and McTavish,  Emily Jane},
+  year = 2021,
+  month = jun,
+  journal = {BMC Bioinformatics},
+  publisher = {Springer Science and Business Media LLC},
+  volume = 22,
+  number = 1,
+  doi = {10.1186/s12859-021-04274-6},
+  issn = {1471-2105},
+  url = {http://dx.doi.org/10.1186/s12859-021-04274-6},
+}
+@article{stamatakis2014raxml,
+  title = {RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies},
+  author = {Stamatakis,  Alexandros},
+  year = 2014,
+  month = jan,
+  journal = {Bioinformatics},
+  publisher = {Oxford University Press (OUP)},
+  volume = 30,
+  number = 9,
+  pages = {1312--1313},
+  doi = {10.1093/bioinformatics/btu033},
+  issn = {1367-4803},
+  url = {http://dx.doi.org/10.1093/bioinformatics/btu033},
+}
+@article{sukumaran2010dendropy,
+  title = {DendroPy: a Python library for phylogenetic computing},
+  author = {Sukumaran,  Jeet and Holder,  Mark T.},
+  year = 2010,
+  month = apr,
+  journal = {Bioinformatics},
+  publisher = {Oxford University Press (OUP)},
+  volume = 26,
+  number = 12,
+  pages = {1569--1571},
+  doi = {10.1093/bioinformatics/btq228},
+  issn = {1367-4803},
+  url = {http://dx.doi.org/10.1093/bioinformatics/btq228},
+}
+@article{vos2012nexml,
+  title = {NeXML: Rich,  Extensible,  and Verifiable Representation of Comparative Data and Metadata},
+  author = {Vos,  Rutger A. and Balhoff,  James P. and Caravas,  Jason A. and Holder,  Mark T. and Lapp,  Hilmar and Maddison,  Wayne P. and Midford,  Peter E. and Priyam,  Anurag and Sukumaran,  Jeet and Xia,  Xuhua and Stoltzfus,  Arlin},
+  year = 2012,
+  month = feb,
+  journal = {Systematic Biology},
+  publisher = {Oxford University Press (OUP)},
+  volume = 61,
+  number = 4,
+  pages = {675--689},
+  doi = {10.1093/sysbio/sys025},
+  issn = {1063-5157},
+  url = {http://dx.doi.org/10.1093/sysbio/sys025},
+}
+@article{wilgenbusch2003inferring,
+  title = {Inferring Evolutionary Trees with PAUP*},
+  author = {Wilgenbusch,  James C. and Swofford,  David},
+  year = 2003,
+  month = jan,
+  journal = {Current Protocols in Bioinformatics},
+  publisher = {Wiley},
+  volume = {00},
+  number = 1,
+  doi = {10.1002/0471250953.bi0604s00},
+  issn = {1934-340x},
+  url = {http://dx.doi.org/10.1002/0471250953.bi0604s00},
 }