---
name: "pplacer"
section: "1"
platform: "linux"
package: "pplacer"
version: "1.1~alpha19-4"
release: "Debian 11 (Bullseye)"
platforms: ["linux"]
url: "https://new.carta.tech/pplacer"
---

# pplacer(1)

place reads on a phylogenetic tree

## NAME

pplacer - place reads on a phylogenetic tree

## SYNOPSIS

**pplacer** \[options\] \[alignment\]

## OPTIONS

- **-c**

  Specify the path to the reference package.

- **-t**

  Specify the reference tree filename.

- **-r**

  Specify the reference alignment filename.

- **-s**

  Supply a phyml stats.txt or a RAxML info file giving the model parameters.

- **-d**

  Specify the directory containing the reference information.

- **-p**

  Calculate posterior probabilities.

- **-m**

  Substitution model. Protein: LG, WAG, or JTT. Nucleotides: GTR.

- **--model-freqs**

  Use model frequencies instead of reference alignment frequencies.

- **--gamma-cats**

  Number of categories for discrete gamma model.

- **--gamma-alpha**

  Specify the shape parameter for a discrete gamma model.

- **--ml-tolerance**

  1st stage branch len optimization tolerance (2nd stage to 1e-5). Default: 0.01.

- **--pp-rel-err**

  Relative error for the posterior probability calculation. Default is 0.01.

- **--unif-prior**

  Use a uniform prior rather than exponential.

- **--inform-prior**

  Use an informative exponential prior based on rooted distance to leaves.

- **--prior-lower**

  Lower bound for the informative prior mean. Default is 0.

- **--start-pend**

  Starting pendant branch length. Default is 0.1.

- **--max-pend**

  Set the maximum ML pendant branch length. Default is 2.

- **--fig-cutoff**

  The cutoff for determining figs. Default is 0; specify 0 to disable.

- **--fig-eval-all**

  Evaluate all likelihoods to ensure that the best location was selected.

- **--fig-eval-discrepancy-tree**

  Write out a tree showing the discrepancies between the best complete and observed locations.

- **--fig-tree**

  Write out a tree showing the figs on the tree.

- **--max-strikes**

  Maximum number of strikes for baseball. 0 -\> no ball playing. Default is 6.

- **--strike-box**

  Set the size of the strike box in log likelihood units. Default is 3.

- **--max-pitches**

  Set the maximum number of pitches for baseball. Default is 40.

- **--fantasy**

  Desired likelihood cutoff for fantasy baseball mode. 0 -\> no fantasy.

- **--fantasy-frac**

  Fraction of fragments to use when running fantasy baseball. Default is 0.1.

- **--write-masked**

  Write alignment masked to the region without gaps in the query.

- **--verbosity**

  Set verbosity level. 0 is silent, and 2 is quite a lot. Default is 1.

- **--out-dir**

  Specify the directory to write place files to.

- **-o**

  Specify the output file name

- **--pretend**

  Only check out the files then report. Do not run the analysis.

- **--check-like**

  Write out the likelihood of the reference tree, calculated two ways.

- **-j**

  The number of child processes to spawn when doing placements. Default is 2.

- **--timing**

  Display timing information after the pplacer run finishes.

- **--no-pre-mask**

  Don't pre-mask sequences before placement.

- **--write-pre-masked**

  Write out the pre-masked sequences to the specified fasta file before placement.

- **--map-mrca**

  Specify a file to write out MAP sequences for MRCAs and corresponding placements.

- **--map-mrca-min**

  Specify cutoff for inclusion in MAP sequence file. Default is 0.8.

- **--map-identity**

  Add the percent identity of the query sequence to the nearest MAP sequence to each placement.

- **--keep-at-most**

  The maximum number of placements we keep. Default is 7.

- **--keep-factor**

  Throw away anything that has ml\_ratio below keep\_factor times (best ml\_ratio). Default is 0.01.

- **--mrca-class**

  Classify with MRCAs instead of a painted tree.

- **--groups**

  Split query alignment into the specified number of groups.

- **--always-refine**

  Always refine the model before placing.

- **--mmap-file**

  Instead of doing large allocations, mmap the given file. It will be created if it doesn't exist.

- **--discard-nonoverlapped**

  When pre-masking, silently discard sequences which don't overlap the mask.

- **--version**

  Write out the version number and exit.

- **-help**

  Display this list of options

- **--help**

  Display this list of options

## AUTHOR

 This manpage was written by Andreas Tille for the Debian distribution and\
  can be used for any other usage of the program.