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

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