pplacer documentation home

The pplacer suite consists of three separate binaries: pplacer, guppy, and rppr. The pplacer binary actually does phylogenetic placement and produces place files, guppy does all of the downstream analysis of placements, and rppr does useful things having to do with reference packages. If this is your first time looking at this documentation we suggest looking at our overview.

Precompiled binaries for Mac OS X and Linux can be found on the the GitHub releases page.

• pplacer
  • Options
  • Details
• guppy
  • Introduction
  • Usage
  • List of subcommands
• rppr
  • Usage
  • List of subcommands
• scripts
  • Installing
  • refpkg_align.py
  • sort_placefile.py
  • update_refpkg.py
  • check_placements.py
  • deduplicate_sequences.py
  • pca_for_qiime.py
  • extract_taxonomy_from_biom.py
  • hrefpkg_query.py
  • multiclass_concat.py
  • split_qiime.py
• glossary
• Compiling pplacer from source
• Changelog

Warning

pplacer is no longer under development. Here are some things that people have used the pplacer suite for:

• placement and visualization
• Kantorovich-Rubenstein distances
• edge principal components and squash clustering
• taxonomic/phylogenetic discordance analysis
• taxon subsetting by minimizing the average distance to the closest leaf
• taxonomic classification

Tutorial

We have made a tutorial available that demonstrates most of the functionality of the pplacer suite of programs. It can be downloaded and run as a shell script.

Getting help

Your question might be covered in the pplacer FAQ already:

• FAQ
  • How can I cite pplacer?
  • Why is pplacer taking up so much memory?
  • Why doesn’t pplacer output a Newick tree?

Otherwise, support for pplacer happens through the user group. If something is unclear in the manual and you can’t find anything in past discussions, post to the group and we will get back to you right away.

Acknowledgements

The pplacer code and documentation is written and maintained by the Matsen group at the Fred Hutchinson Cancer Research Center. Noah Hoffman has contributed many valuable ideas and bits of documentation. We are greatly indebted to our biological collaborators, including Ginger Armbrust, David Fredricks, Robin Kodner, Martin Morgan, and Sujatha Srivnasan for their suggestions.