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phylogenetics moved era genomics incorporating enormous volumes data study questions shallow deep scales increase information phylogeneticists need new tools skills manipulate analyze data facilitate tasks encourage reproducibility community increasingly moving toward automated workflows present pipesnake phylogenomics pipeline written nextflow processing assembly phylogenetic estimation genomic data shortread sequences pipesnake easy use efficient software package designed next era phylogenetics pipesnake publicly available github httpsgithubcomausargpipesnake accompanied documentation wikitutorial