About PEPPA PEPPA (Phylogeny Enhanced Pipeline for PAn-genome) is a pipeline that can construct a pan-genome from thousands of genetically diversified bacterial genomes. PEPPA implements a combination of tree- and synteny-based approaches to identify and exclude paralogous genes, as well as similarity-based gene predictions that support consistent annotations of genes and pseudogenes in individual genomes.
Citation If you use GrapeTree please cite the pre-print in BioRxiv:
Z Zhou, M Achtman (2020) "Accurate reconstruction of the pan- and core- genomes of bacteria with PEPPA" bioRxiv, doi: https://doi.org/10.1101/2020.01.03.894154 <https://doi.org/10.1101/2020.01.03.894154>_
installation <docs/source/usage/installation.rst>_quickstart <docs/source/usage/quickstart.rst>_parameters <docs/source/usage/parameters.rst>_inputs <docs/source/usage/inputs.rst>_outputs <docs/source/usage/outputs.rst>_
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