guppy - Grand Unified Phylogenetic Placement Yanalyzer - yanalyzes
pplacer output
guppy <command> [options]
- 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
- 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
- classify
- outputs classification information in SQLite format
- to_rdp
- convert a reference package to a format RDP wants
- 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
- --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
This manpage was written by Andreas Tille for the Debian
distribution and
can be used for any other usage of the program.