PEPPAN

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About PEPPAN PEPPAN (Phylogeny Enhanced Pipeline for PAN-genome) is a pipeline that can construct a pan-genome from thousands of genetically diversified bacterial genomes. PEPPAN 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 PEPPAN 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>_