guppy(1)

guppy1

Grand unified phylogenetic placement yanalyzer - yanalyzes pplacer output

Usage

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