main.bbl

\begin{thebibliography}{10}

\bibitem{monovar}
Hamim Zafar, Yong Wang, Luay Nakhleh, Nicholas Navin, and Ken Chen.
\newblock Monovar: single-nucleotide variant detection in single cells.
\newblock {\em Nature methods}, 13(6):505, 2016.

\bibitem{sciphi}
Jochen Singer, Jack Kuipers, Katharina Jahn, and Niko Beerenwinkel.
\newblock Single-cell mutation identification via phylogenetic inference.
\newblock {\em Nature communications}, 9(1):5144, 2018.

\bibitem{BSA}
Richard Durbin, Sean~R Eddy, Anders Krogh, and Graeme Mitchison.
\newblock {\em Biological sequence analysis: probabilistic models of proteins
  and nucleic acids}.
\newblock Cambridge university press, 1998.

\bibitem{NJ}
Naruya Saitou and Masatoshi Nei.
\newblock The neighbor-joining method: a new method for reconstructing
  phylogenetic trees.
\newblock {\em Molecular biology and evolution}, 4(4):406--425, 1987.

\bibitem{EmperorMaladies}
Siddhartha Mukherjee.
\newblock {\em The emperor of all maladies: a biography of cancer}.
\newblock Simon and Schuster, 2010.

\bibitem{bigbang}
Andrea Sottoriva, Haeyoun Kang, Zhicheng Ma, Trevor~A Graham, Matthew~P
  Salomon, Junsong Zhao, Paul Marjoram, Kimberly Siegmund, Michael~F Press,
  Darryl Shibata, et~al.
\newblock A big bang model of human colorectal tumor growth.
\newblock {\em Nature genetics}, 47(3):209, 2015.

\bibitem{metastatic}
Gunes Gundem, Peter Van~Loo, Barbara Kremeyer, Ludmil~B Alexandrov, Jose~MC
  Tubio, Elli Papaemmanuil, Daniel~S Brewer, Heini~ML Kallio, Gunilla
  H{\"o}gn{\"a}s, Matti Annala, et~al.
\newblock The evolutionary history of lethal metastatic prostate cancer.
\newblock {\em Nature}, 520(7547):353, 2015.

\bibitem{21breasts}
Serena Nik-Zainal, Peter Van~Loo, David~C Wedge, Ludmil~B Alexandrov,
  Christopher~D Greenman, King~Wai Lau, Keiran Raine, David Jones, John
  Marshall, Manasa Ramakrishna, et~al.
\newblock The life history of 21 breast cancers.
\newblock {\em Cell}, 149(5):994--1007, 2012.

\bibitem{21breasts2}
Serena Nik-Zainal, Ludmil~B Alexandrov, David~C Wedge, Peter Van~Loo,
  Christopher~D Greenman, Keiran Raine, David Jones, Jonathan Hinton, John
  Marshall, Lucy~A Stebbings, et~al.
\newblock Mutational processes molding the genomes of 21 breast cancers.
\newblock {\em Cell}, 149(5):979--993, 2012.

\bibitem{greaves2012clonal}
Mel Greaves and Carlo~C Maley.
\newblock Clonal evolution in cancer.
\newblock {\em Nature}, 481(7381):306, 2012.

\bibitem{merlo2006cancer}
Lauren~MF Merlo, John~W Pepper, Brian~J Reid, and Carlo~C Maley.
\newblock Cancer as an evolutionary and ecological process.
\newblock {\em Nature reviews cancer}, 6(12):924, 2006.

\bibitem{aneuploidy}
Harith Rajagopalan and Christoph Lengauer.
\newblock Aneuploidy and cancer.
\newblock {\em Nature}, 432(7015):338, 2004.

\bibitem{sequencesequencers}
James~M Heather and Benjamin Chain.
\newblock The sequence of sequencers: The history of sequencing dna.
\newblock {\em Genomics}, 107(1):1--8, 2016.

\bibitem{massivelyparallel}
Tracy Tucker, Marco Marra, and Jan~M Friedman.
\newblock Massively parallel sequencing: the next big thing in genetic
  medicine.
\newblock {\em The American Journal of Human Genetics}, 85(2):142--154, 2009.

\bibitem{SCSadvance}
Yong Wang and Nicholas~E Navin.
\newblock Advances and applications of single-cell sequencing technologies.
\newblock {\em Molecular cell}, 58(4):598--609, 2015.

\bibitem{scprimer}
Tal Nawy.
\newblock Single-cell sequencing.
\newblock {\em Nature methods}, 11(1):18, 2013.

\bibitem{clonevol}
HX~Dang, BS~White, SM~Foltz, CA~Miller, Jingqin Luo, RC~Fields, and CA~Maher.
\newblock Clonevol: clonal ordering and visualization in cancer sequencing.
\newblock {\em Annals of oncology}, 28(12):3076--3082, 2017.

\bibitem{onecelltime}
Nicholas~E Navin.
\newblock Cancer genomics: one cell at a time.
\newblock {\em Genome biology}, 15(8):452, 2014.

\bibitem{rnaseq}
Zhong Wang, Mark Gerstein, and Michael Snyder.
\newblock Rna-seq: a revolutionary tool for transcriptomics.
\newblock {\em Nature reviews genetics}, 10(1):57, 2009.

\bibitem{cellity}
Tomislav Ilicic, Jong~Kyoung Kim, Aleksandra~A Kolodziejczyk, Frederik~Otzen
  Bagger, Davis~James McCarthy, John~C Marioni, and Sarah~A Teichmann.
\newblock Classification of low quality cells from single-cell rna-seq data.
\newblock {\em Genome biology}, 17(1):29, 2016.

\bibitem{biochemistry}
J.M. Berg, J.L. Tymoczko, and L.~Stryer.
\newblock {\em Biochemistry}.
\newblock Biochemistry (Berg). W. H. Freeman, 2007.

\bibitem{gao2016punctuated}
Ruli Gao, Alexander Davis, Thomas~O McDonald, Emi Sei, Xiuqing Shi, Yong Wang,
  Pei-Ching Tsai, Anna Casasent, Jill Waters, Hong Zhang, et~al.
\newblock Punctuated copy number evolution and clonal stasis in triple-negative
  breast cancer.
\newblock {\em Nature genetics}, 48(10):1119, 2016.

\bibitem{greenman2007patterns}
Christopher Greenman, Philip Stephens, Raffaella Smith, Gillian~L Dalgliesh,
  Christopher Hunter, Graham Bignell, Helen Davies, Jon Teague, Adam Butler,
  Claire Stevens, et~al.
\newblock Patterns of somatic mutation in human cancer genomes.
\newblock {\em Nature}, 446(7132):153, 2007.

\bibitem{alexandrov2013signatures}
Ludmil~B Alexandrov, Serena Nik-Zainal, David~C Wedge, Samuel~AJR Aparicio, Sam
  Behjati, Andrew~V Biankin, Graham~R Bignell, Niccolo Bolli, Ake Borg,
  Anne-Lise B{\o}rresen-Dale, et~al.
\newblock Signatures of mutational processes in human cancer.
\newblock {\em Nature}, 500(7463):415, 2013.

\bibitem{JC}
Thomas~H Jukes, Charles~R Cantor, et~al.
\newblock Evolution of protein molecules.
\newblock {\em Mammalian protein metabolism}, 3(21):132, 1969.

\bibitem{neutralevoltumour}
Marc~J Williams, Benjamin Werner, Chris~P Barnes, Trevor~A Graham, and Andrea
  Sottoriva.
\newblock Identification of neutral tumor evolution across cancer types.
\newblock {\em Nature genetics}, 48(3):238, 2016.

\bibitem{numcells}
Ugo Del~Monte.
\newblock Does the cell number $10^9$ still really fit one gram of tumor
  tissue?
\newblock {\em Cell Cycle}, 8(3):505--506, 2009.

\bibitem{yachida}
Shinichi Yachida, Si{\^a}n Jones, Ivana Bozic, Tibor Antal, Rebecca Leary,
  Baojin Fu, Mihoko Kamiyama, Ralph~H Hruban, James~R Eshleman, Martin~A Nowak,
  et~al.
\newblock Distant metastasis occurs late during the genetic evolution of
  pancreatic cancer.
\newblock {\em Nature}, 467(7319):1114, 2010.

\bibitem{listatistical}
Heng Li.
\newblock A statistical framework for snp calling, mutation discovery,
  association mapping and population genetical parameter estimation from
  sequencing data.
\newblock {\em Bioinformatics}, 27(21):2987--2993, 2011.

\bibitem{ledurbin}
Si~Quang Le and Richard Durbin.
\newblock {SNP} detection and genotyping from low-coverage sequencing data on
  multiple diploid samples.
\newblock {\em Genome research}, 21(6):952--960, 2011.

\bibitem{negedge}
Mary~K Kuhner and Joseph Felsenstein.
\newblock A simulation comparison of phylogeny algorithms under equal and
  unequal evolutionary rates.
\newblock {\em Molecular biology and evolution}, 11(3):459--468, 1994.

\bibitem{RFmetric}
David~F Robinson and Leslie~R Foulds.
\newblock Comparison of phylogenetic trees.
\newblock {\em Mathematical biosciences}, 53(1-2):131--147, 1981.

\bibitem{TreeCmp}
Damian Bogdanowicz, Krzysztof Giaro, and Borys Wr{\'o}bel.
\newblock Treecmp: comparison of trees in polynomial time.
\newblock {\em Evolutionary Bioinformatics}, 8:EBO--S9657, 2012.

\bibitem{BWAMEM}
Heng Li.
\newblock Aligning sequence reads, clone sequences and assembly contigs with
  bwa-mem.
\newblock {\em arXiv preprint arXiv:1303.3997}, 2013.

\bibitem{missingNJ}
Vladimir Makarenkov and Fran{\c{c}}ois-Joseph Lapointe.
\newblock A weighted least-squares approach for inferring phylogenies from
  incomplete distance matrices.
\newblock {\em Bioinformatics}, 20(13):2113--2121, 2004.

\bibitem{samtools}
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor
  Marth, Goncalo Abecasis, and Richard Durbin.
\newblock The sequence alignment/map format and samtools.
\newblock {\em Bioinformatics}, 25(16):2078--2079, 2009.

\bibitem{gatk1}
Mark~A DePristo, Eric Banks, Ryan Poplin, Kiran~V Garimella, Jared~R Maguire,
  Christopher Hartl, Anthony~A Philippakis, Guillermo Del~Angel, Manuel~A
  Rivas, Matt Hanna, et~al.
\newblock A framework for variation discovery and genotyping using
  next-generation dna sequencing data.
\newblock {\em Nature genetics}, 43(5):491, 2011.

\bibitem{gatk2}
Geraldine~A Van~der Auwera, Mauricio~O Carneiro, Christopher Hartl, Ryan
  Poplin, Guillermo Del~Angel, Ami Levy-Moonshine, Tadeusz Jordan, Khalid
  Shakir, David Roazen, Joel Thibault, et~al.
\newblock From fastq data to high-confidence variant calls: the genome analysis
  toolkit best practices pipeline.
\newblock {\em Current protocols in bioinformatics}, 43(1):11--10, 2013.

\bibitem{DATA}
Yong Wang, Jill Waters, Marco~L Leung, Anna Unruh, Whijae Roh, Xiuqing Shi, Ken
  Chen, Paul Scheet, Selina Vattathil, Han Liang, et~al.
\newblock Clonal evolution in breast cancer revealed by single nucleus genome
  sequencing.
\newblock {\em Nature}, 512(7513):155, 2014.

\bibitem{sciclone}
Christopher~A Miller, Brian~S White, Nathan~D Dees, Malachi Griffith, John~S
  Welch, Obi~L Griffith, Ravi Vij, Michael~H Tomasson, Timothy~A Graubert,
  Matthew~J Walter, et~al.
\newblock Sci{C}lone: inferring clonal architecture and tracking the spatial
  and temporal patterns of tumor evolution.
\newblock {\em PLoS computational biology}, 10(8):e1003665, 2014.

\end{thebibliography}