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

# guppy(1)

Grand Unified Phylogenetic Placement Yanalyzer - yanalyzes pplacer output

## NAME

guppy - Grand Unified Phylogenetic Placement Yanalyzer - yanalyzes pplacer output

## SYNOPSIS

**guppy** \<command\> \[options\]

## OPTIONS

### visualization

- fat

  makes trees with edges fattened in proportion to the number of reads

- heat

  maps an an arbitrary vector of the correct length to the tree

- sing

  makes one tree for each query sequence, showing uncertainty

- tog

  makes a tree with each of the reads represented as a pendant edge

### statistical comparison

- bary

  draws the barycenter of a placement collection on the reference tree

- edpl

  calculates the EDPL uncertainty values for a collection of pqueries

- epca

  performs edge principal components

- error

  finds the error between two placefiles

- fpd

  calculates various alpha diversity metrics of placefiles

- indep\_c

  calculates the independent contrasts of pqueries

- kr

  calculates the Kantorovich-Rubinstein distance and corresponding p-values

- kr\_heat

  makes a heat tree

- lpca

  performs length principal components

- mcl

  cluster pqueries using Markov clustering via MCL

- pmlpca

  performs poor-man's length principal components

- rarefact

  calculates phylogenetic rarefaction curves

- splitify

  writes out differences of masses for the splits of the tree

- squash

  performs squash clustering

- unifrac

  calculates unifrac on two or more placefiles

## classification

- classify

  outputs classification information in SQLite format

- to\_rdp

  convert a reference package to a format RDP wants

### utilities

- adcl

  calculates ADCL for each pquery in a placefile

- check

  checks placefiles for common problems

- compress

  compresses a placefile's pqueries

- demulti

  splits apart placements with multiplicity, undoing a round procedure

- distmat

  prints out a pairwise distance matrix between the edges

- filter

  filters one or more placefiles by placement name

- info

  writes the number of leaves of the reference tree and the number of pqueries

- islands

  finds the mass islands of one or more pqueries

- merge

  merges placefiles together

- mft

  Multi-Filter and Transform placefiles

- ograph

  finds the overlap graph of one or more pqueries

- placemat

  prints out a pairwise distance matrix between placements

- rarefy

  performs rarefaction on collections of placements

- redup

  restores duplicates to deduped placefiles

- round

  clusters the placements by rounding branch lengths

- to\_csv

  turns a placefile into a csv file

- to\_json

  converts old-style .place files to .jplace placement files

- trim

  trims placefiles down to only containing an informative subset of the mass

To get more help about a given command, type guppy COMMAND **--help**

### Additional options

- **--version**

  Print version and exit

- **--cmds**

  Print a list of the available commands.

- **--batch**

  Run the provided batch file of guppy commands

- **--quiet**

  Don't write messages to stdout (unless explicitly requested).

- **--help**

  Display this list of options and subcommands

- **-help**

  Display this list of options and subcommands

## AUTHOR

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