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SUMMARY With the explosive growth of bacterial and archaeal sequence data, large-scale phylogenetic analyses present both opportunities and challenges. Here we describe AMPHORA2, an automated phylogenomic inference tool that can be used for high-throughput, high-quality genome tree reconstruction and metagenomic phylotyping. Compared with its predecessor,(More)
Structural variants (SVs) are an important source of human genetic diversity, but their contribution to traits, disease and gene regulation remains unclear. We mapped cis expression quantitative trait loci (eQTLs) in 13 tissues via joint analysis of SVs, single-nucleotide variants (SNVs) and short insertion/deletion (indel) variants from deep whole-genome(More)
17 Rare genetic variants are abundant in humans yet their functional effects are often unknown and 18 challenging to predict. The Genotype-Tissue Expression (GTEx) project provides a unique opportunity to 19 identify the functional impact of rare variants through combined analyses of whole genomes and multi-20 tissue RNA-sequencing data. Here, we identify(More)
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