Concepedia

Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX

Mikkel Schubert, Luca Ermini, Clio Der Sarkissian, Hákon Jónsson, Aurélien Ginolhac, Robert Schaefer, Michael D. Martin, Ruth Fernández, Martin Kircher, Molly E. McCue,

Nature Protocols · 2014 · 571 citations · 66 references

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References

66

The Sequence Alignment/Map format and SAMtools

Heng Li, Alec Wysoker, Tim Fennell et al. · Bioinformatics · 2009 · 67.5K citations · Full text

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Fast and accurate short read alignment with Burrows–Wheeler transform

Heng Li, Richard Durbin · Bioinformatics · 2009 · 62.8K citations · Full text

, , +12

Fast gapped-read alignment with Bowtie 2

Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 61.1K citations

, , +11

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh, Daron M. Standley · Molecular Biology and Evolution · 2013 · 48.3K citations · Full text

, , +11

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan, Ira M. Hall · Bioinformatics · 2010 · 30.4K citations · Full text

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