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@article{jaffe2012fastg,
title = {{The FASTG Format Specification (v1.00). http}},
author = {Jaffe, DB and others},
url = {http://fastg.sourceforge.net/FASTG_Spec_v1.00.pdf},
year = {2012}
}
@misc{FASTAformat,
author = {NCBI},
title = {{Accepted input formats}},
url = {http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml},
year = {Accessed: 2015-08-06},
}
@article{comm1970abbreviations,
title = {{Abbreviations and symbols for nucleic acids, polynucleotides, and their constituents}},
author = {Comm, IUPAC-IUB},
journal = {Biochemistry},
volume = {9},
number = {20},
pages = {4022--4027},
year = {1970},
publisher = {ACS Publications},
}
@article{langmead2012fast,
title = {{Fast gapped-read alignment with Bowtie 2}},
author = {Langmead, Ben and Salzberg, Steven L},
journal = {Nature methods},
volume = {9},
number = {4},
pages = {357--359},
year = {2012},
publisher = {Nature Publishing Group},
}
@article{bolger2014trimmomatic,
title = {{Trimmomatic: a flexible trimmer for Illumina sequence data}},
author = {Bolger, Anthony M and Lohse, Marc and Usadel, Bjoern},
journal = {Bioinformatics},
pages = {btu170},
year = {2014},
publisher = {Oxford Univ Press},
}
@article{PMID:10827456,
title = {{EMBOSS: the European Molecular Biology Open Software Suite}},
author = {Rice, P and Longden, I and Bleasby, A},
doi = {10.1016/s0168-9525(00)02024-2},
number = {6},
volume = {16},
month = {June},
year = {2000},
journal = {Trends in genetics : TIG},
issn = {0168-9525},
pages = {276—277},
url = {http://dx.doi.org/10.1016/S0168-9525(00)02024-2},
}
@misc{Li2013,
key = {Li, H., seqtk GitHub repository },
title = {Li, H., seqtk GitHub repository, 4feb6e81444ab6bc44139dd3a125068f81ae4ad8},
url = {https://github.com/lh3/seqtk}
}
@article{bioperl,
author = {Stajich, J. E. and Block, D. and Boulez, K. and Brenner, S. E. and Chervitz, S. A. and Dagdigian, C. and Fuellen, G. and Gilbert, J. G. and Korf, I. and Lapp, H. and Lehvaslaiho, H. and Matsalla, C. and Mungall, C. J. and Osborne, B. I. and Pocock, M. R. and Schattner, P. and Senger, M. and Stein, L. D. and Stupka, E. and Wilkinson, M. D. and Birney, E.},
journal = {Genome Res},
number = {10},
pages = {1611--8},
title = {{The {B}ioperl toolkit: {P}erl modules for the life sciences.}},
volume = {12},
year = {2002},
}
@article{bioperl2,
author = {Stein, L. D. and Mungall, C. and Shu, S. and Caudy, M. and Mangone, M. and Day, A. and Nickerson, E. and Stajich, J. E. and Harris, T. W. and Arva, A. and Lewis, S.},
journal = {Genome Res},
number = {10},
pages = {1599--610},
title = {{The generic genome browser: a building block for a model organism system database.}},
volume = {12},
year = {2002},
}
@article{bioperl3,
author = {Stajich, Jason E. and Hahn, Matthew W.},
doi = {10.1093/molbev/msh252},
issn = {0737-4038},
journal = {Molecular biology and evolution},
month = {jan},
number = {1},
pages = {63--73},
pmid = {15356276},
title = {{Disentangling the effects of demography and selection in human history.}},
url = {http://dx.doi.org/10.1093/molbev/msh252},
volume = {22},
year = {2005},
}
@article{Lindblad_Toh_2011,
doi = {10.1038/nature10530},
url = {http://dx.doi.org/10.1038/nature10530},
year = {2011},
month = {oct},
publisher = {Nature Publishing Group},
volume = {478},
number = {7370},
pages = {476--482},
author = {Kerstin Lindblad-Toh and Manuel Garber and Or Zuk and Michael F. Lin and Brian J. Parker and Stefan Washietl and Pouya Kheradpour and Jason Ernst and Gregory Jordan and Evan Mauceli and Lucas D. Ward and Craig B. Lowe and Alisha K. Holloway and Michele Clamp and Sante Gnerre and Jessica Alföldi and Kathryn Beal and Jean Chang and Hiram Clawson and James Cuff and Federica Di Palma and Stephen Fitzgerald and Paul Flicek and Mitchell Guttman and Melissa J. Hubisz and David B. Jaffe and Irwin Jungreis and W. James Kent and Dennis Kostka and Marcia Lara and Andre L. Martins and Tim Massingham and Ida Moltke and Brian J. Raney and Matthew D. Rasmussen and Jim Robinson and Alexander Stark and Albert J. Vilella and Jiayu Wen and Xiaohui Xie and Michael C. Zody and Jen Baldwin and Toby Bloom and Chee Whye Chin and Dave Heiman and Robert Nicol and Chad Nusbaum and Sarah Young and Jane Wilkinson and Kim C. Worley and Christie L. Kovar and Donna M. Muzny and Richard A. Gibbs and Andrew Cree and Huyen H. Dihn and Gerald Fowler and Shalili Jhangiani and Vandita Joshi and Sandra Lee and Lora R. Lewis and Lynne V. Nazareth and Geoffrey Okwuonu and Jireh Santibanez and Wesley C. Warren and Elaine R. Mardis and George M. Weinstock and Richard K. Wilson and Kim Delehaunty and David Dooling and Catrina Fronik and Lucinda Fulton and Bob Fulton and Tina Graves and Patrick Minx and Erica Sodergren and Ewan Birney and Elliott H. Margulies and Javier Herrero and Eric D. Green and David Haussler and Adam Siepel and Nick Goldman and Katherine S. Pollard and Jakob S. Pedersen and Eric S. Lander and Manolis Kellis},
title = {{A high-resolution map of human evolutionary constraint using 29 mammals}},
journal = {Nature},
}
@article{blank,
author = {},
title = {},
journal = {},
year = {},
month = {},
volume= {},
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pages = {},
note = {}
}
