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@misc{divsufsort,
author="Yuta Mori",
year="2005",
title="Short description of improved two-stage suffix sorting algorithm",
note="\url{http://homepage3.nifty.com/wpage/software/itssort.txt}"
}
@article{andi,
author = {Haubold, Bernhard and Klötzl, Fabian and Pfaffelhuber, Peter},
title = {andi: Fast and accurate estimation of evolutionary distances between closely related genomes},
volume = {31},
number = {8},
pages = {1169-1175},
year = {2015},
doi = {10.1093/bioinformatics/btu815},
URL = {http://bioinformatics.oxfordjournals.org/content/31/8/1169.abstract},
eprint = {http://bioinformatics.oxfordjournals.org/content/31/8/1169.full.pdf+html},
journal = {Bioinformatics}
}
@book{Felsenstein,
author={Joseph Felsenstein},
title={Inferring Phylogenies},
year={2004},
publisher={Sinauer Associates, Inc.}
}
@misc{GPL,
author={{Free~Software~Foundation}},
year={2007},
title={Gnu General Public License},
note={\url{https://gnu.org/licenses/gpl.html}}
}
@misc{phylip,
author={Felsenstein, J.},
year={2005},
title={PHYLIP (Phylogeny Inference Package)},
version={version 3.6},
howpublished={Distributed by the author},
note={Department of Genome Sciences, University of Washington.}
}
@InProceedings{LLVM,
Author = {Chris Lattner and Vikram Adve},
Title = {{LLVM}: A Compilation Framework for Lifelong Program
Analysis and Transformation},
Booktitle = "Code Generation and Optimization",
Month = {Mar},
Year = {2004},
pages = {75--88},
Publisher={International Symposium on Code Generation and Optimization}
}
@article{ms,
author = {Hudson, Richard R.},
title = {Generating samples under a Wright–Fisher neutral model of genetic variation},
volume = {18},
number = {2},
pages = {337-338},
year = {2002},
doi = {10.1093/bioinformatics/18.2.337},
URL = {http://bioinformatics.oxfordjournals.org/content/18/2/337.abstract},
eprint = {http://bioinformatics.oxfordjournals.org/content/18/2/337.full.pdf+html},
journal = {Bioinformatics}
}
@article{valgrind,
author = {Nethercote, Nicholas and Seward, Julian},
title = {Valgrind: A Framework for Heavyweight Dynamic Binary Instrumentation},
journal = {SIGPLAN Not.},
issue_date = {June 2007},
volume = {42},
number = {6},
month = jun,
year = {2007},
issn = {0362-1340},
pages = {89--100},
numpages = {12},
url = {http://doi.acm.org/10.1145/1273442.1250746},
doi = {10.1145/1273442.1250746},
acmid = {1250746},
publisher = {ACM},
keywords = {Memcheck, Valgrind, dynamic binary analysis, dynamic binary instrumentation, shadow values}
}
@misc{figtree,
title="FigTree",
author={Andrew Rambaut},
year={accessed 2015},
note={\url{http://tree.bio.ed.ac.uk/software/figtree/}}
}
@article{jukescantor,
author={Jukes, T. H. and Cantor, C. R.},
year={1969},
title={Evolution of protein molecules},
journal={Mammalian protein metabolism},
volume={3},
pages={21-132},
publisher={Academic Press}
}
@mastersthesis{kloetzl,
author={Fabian Kl{\"o}tzl},
school={University of L\"ubeck},
year={2015},
title={Efficient Estimation of Evolutionary Distances}
}
@article{afra,
AUTHOR = {Klötzl, Fabian and Haubold, Bernhard},
TITLE = {Support Values for Genome Phylogenies},
JOURNAL = {Life},
VOLUME = {6},
YEAR = {2016},
NUMBER = {1},
PAGES = {11},
URL = {http://www.mdpi.com/2075-1729/6/1/11},
ISSN = {2075-1729},
DOI = {10.3390/life6010011}
}
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