[Alexander2009]Alexander et al. “Fast model-based estimation of ancestry in unrelated individuals”. Genome Res. 2009 Sep;19(9):1655-64. doi:10.1101/gr.094052.109
[Chang2015]Chang et al. “Second-generation PLINK: rising to the challenge of larger and richer datasets”. Gigascience. 2015 Feb 25;4:7. doi: 10.1186/s13742-015-0047-8
[Daley2013]Daley and Smith. “Predicting the molecular complexity of sequencing libraries”. Nat Methods. 2013 Apr;10(4):325-7. doi:10.1038/nmeth.2375
[DerSarkissian2015]Der Sarkissian et al. “Evolutionary Genomics and Conservation of the Endangered Przewalski’s Horse”. Curr Biol. 2015 Oct 5;25(19):2577-83. doi:10.1016/j.cub.2015.08.032
[Jonsson2013]Jónsson et al. “mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters”. Bioinformatics. 2013 Jul 1;29(13):1682-4. doi:10.1093/bioinformatics/btt193
[Jonsson2014]Jónsson et al. “Speciation with gene flow in equids despite extensive chromosomal plasticity”. PNAS. 2014 Dec 30;111(52):18655-60. doi:10.1073/pnas.1412627111
[Katoh2013]Katoh and Standley. “MAFFT multiple sequence alignment software version 7: improvements in performance and usability”. Mol Biol Evol. 2013 Apr;30(4):772-80. doi:10.1093/molbev/mst010
[Langmead2012]Langmead and Salzberg. “Fast gapped-read alignment with Bowtie 2”. Nat Methods. 2012 Mar 4;9(4):357-9. doi:10.1038/nmeth.1923
[Li2009a]Li and Durbin. “Fast and accurate short read alignment with Burrows-Wheeler transform”. Bioinformatics. 2009 Jul 15;25(14):1754-60. doi:10.1093/bioinformatics/btp324
[Li2009b]Li et al. “The Sequence Alignment/Map format and SAMtools”. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi:10.1093/bioinformatics/btp352
[Lindgreen2012]Lindgreen. “AdapterRemoval: Easy Cleaning of Next Generation Sequencing Reads”, BMC Research Notes. 2012 Jul 5:337.
[McKenna2010]McKenna et al. “The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data”. Genome Res. 2010 Sep;20(9):1297-303. doi:10.1101/gr.107524.110
[Orlando2013]Orlando et al. “Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse”. Nature. 2013 Jul; 499(7456):74-78. doi:10.1038/nature12323.
[Paradis2004]Paradis et al. “APE: Analyses of Phylogenetics and Evolution in R language”. Bioinformatics. 2004 Jan 22;20(2):289-90. doi:10.1093/bioinformatics/btg412
[Patterson2006]Patterson N, Price AL, Reich D. Population structure and eigenanalysis. PLoS Genet. 2006 Dec;2(12):e190. doi:10.1371/journal.pgen.0020190
[Peltzer2016]Peltzer et al. “EAGER: efficient ancient genome reconstruction”. Genome Biology. 2016 Mar 9; 17:60. doi:10.1186/s13059-016-0918-z
[Pickrell2012]Pickrell and Pritchard. “Inference of population splits and mixtures from genome-wide allele frequency data”. PLoS Genet. 2012;8(11):e1002967. doi:10.1371/journal.pgen.1002967
[Price2006]Price et al. “Principal components analysis corrects for stratification in genome-wide association studies”. Nat Genet. 2006 Aug;38(8):904-9. Epub 2006 Jul 23. doi:10.1038/ng1847
[Quinlan2010]Quinlan and Hall. “BEDTools: a flexible suite of utilities for comparing genomic features”. Bioinformatics. 2010 Mar 15;26(6):841-2. doi:10.1093/bioinformatics/btq033
[Schubert2012]Schubert et al. “Improving ancient DNA read mapping against modern reference genomes”. BMC Genomics. 2012 May 10;13:178. doi:10.1186/1471-2164-13-178.
[Schubert2014]Schubert et al. “Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX”. Nature Protocols. 2014 May;9(5):1056-82. doi:10.1038/nprot.2014.063
[Stamatakis2006]Stamatakis. “RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models”. Bioinformatics. 2006 Nov 1;22(21):2688-90.
[Wickham2007]Wickham. “Reshaping Data with the reshape Package”. Journal of Statistical Software. 2007 21(1).
[Wickham2009]Wichham. “ggplot2: Elegant Graphics for Data Analysis”. Springer-Verlag New York 2009. ISBN:978-0-387-98140-6