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.

guppy 1.1~alpha19                                   June 2020                                           GUPPY(1)