ArticleNature protocols2014
Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX.
Article in Nature protocols, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 253 papers.
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Who cites it
253 citing papers in PubMed, 557 citations in OpenAlex.
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- Genome Scanning Reveals the Genetic Basis of a Color Pattern Morphotype in an Island Population of the European Adder (Vipera berus).Genome biology and evolution · 2026Article
- FALCON2: compression-based metagenomic classification of ancient viruses.Bioinformatics (Oxford, England) · 2026Article
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- The genomic basis of adaptive leaf variation in the Galápagos giant daisies.Nature communications · 2026Article
- Predicting extinction risk of gibbons from genomes of extinct Yunnan lar gibbon.Genome biology · 2026Article
- Ancient DNA reveals 4000 years of grapevine diversity, viticulture and clonal propagation in France.Nature communications · 2026Article
- The Japanese Archipelago sheltered cave lions, not tigers, during the Late Pleistocene.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
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- Patterns of aDNA damage through time and environments-lessons from herbarium specimens.GigaScience · 2026Article
- Population structure and domestication history of the Javan banteng.Current biology : CB · 2026Article
193 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing technologies have revolutionized the field of paleogenomics, allowing the reconstruction of complete ancient genomes and their comparison with modern references. However, this requires the processing of vast amounts of data and involves a large number of steps that use a variety of computational tools. Here we present PALEOMIX (http://geogenetics.ku.dk/publications/paleomix), a flexible and user-friendly pipeline applicable to both modern and ancient genomes, which largely automates the in silico analyses behind whole-genome resequencing. Starting with next-generation sequencing reads, PALEOMIX carries out adapter removal, mapping against reference genomes, PCR duplicate removal, characterization of and compensation for postmortem damage, SNP calling and maximum-likelihood phylogenomic inference, and it profiles the metagenomic contents of the samples. As such, PALEOMIX allows for a series of potential applications in paleogenomics, comparative genomics and metagenomics. Applying the PALEOMIX pipeline to the three ancient and seven modern Phytophthora infestans genomes as described here takes 5 d using a 16-core server.
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