For a detailed description of the pipeline, please refer to PALEOMIX website and the wiki; for up-to-date documentation, please refer to the wiki; for questions, bug reports, and/or suggestions, use the GitHub tracker, or contact Mikkel Schubert at MSchubert@snm.ku.dk.
The PALEOMIX pipeline has been published in Nature Protocols; if you make use of (parts of) the pipeline in your work, then please cite
Schubert M, Ermini L, Sarkissian CD, Jónsson H, Ginolhac A, Schaefer R, Martin MD, Fernández R, Kircher M, McCue M, Willerslev E, and Orlando L. "Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX". Nat Protoc. 2014 May;9(5):1056-82. doi: 10.1038/nprot.2014.063. Epub 2014 Apr 10. PubMed PMID: 24722405.