# Welcome to PEPPA’s documentation!

Contents:

- installation
- quickstart
- parameters
- inputs
- outputs
  - inference=ortholog_group:<source_genome>:<exemplar_gene>:<allele_ID>:<start & end coordinates of alignment in the exemplar gene>:<start & end coordinates of alignmenet in the genome>

## 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)

# Indices and tables

- Index

- Module Index

- Search Page