GUPPY(1)

✨ NAME ✨

guppy — the Grand Unified Phylogenetic Placement Yanalyzer, bestie 💅 it literally yanalyzes your pplacer output. Yes, that's the whole job and she's iconic for it.

🦋 SYNOPSIS 🦋

guppy <command> [options]

💖 OPTIONS 💖

Okay so guppy is basically a whole girl group of subcommands, and they're split into lil cliques. Let me introduce you to everybody 🫶

👑 visualization

• fat — makes trees where the edges get fattened in proportion to the number of reads. chunky tree era fr.
• heat — maps an arbitrary vector of the correct length onto the tree. yes "arbitrary" — she said what she said.
• sing — makes one tree for each query sequence, so you can literally see the uncertainty. one tree per query, no shortcuts ✨
• tog — makes a tree where each of the reads is represented as a pendant edge. cute lil dangly reads.

📊 statistical comparison

• bary — draws the barycenter</bary>... wait no, the barycenter of a placement collection on the reference tree. mathematically gorgeous of her tbh.
• edpl — calculates the EDPL uncertainty values for a collection of pqueries.
• epca — performs edge principal components. PCA but make it edges.
• error — finds the error between two placefiles. snitching, but productively.
• fpd — calculates various alpha diversity metrics of placefiles.
• indep_c — calculates the independent contrasts of pqueries.
• kr — calculates the Kantorovich-Rubinstein distance and the corresponding p-values. a whole mouthful and she EARNED it.
• kr_heat — makes a heat tree 🔥 combining the kr vibe with the heat vibe.
• lpca — performs length principal components. the length-flavored sister of epca.
• mcl — clusters pqueries using Markov clustering via MCL.
• pmlpca — performs poor-man's length principal components. budget queen but she delivers.
• rarefact — calculates phylogenetic rarefaction curves.
• splitify — writes out differences of masses for the splits of the tree.
• squash — performs squash clustering. yes it's really called that, and yes it's a vibe.
• 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. doing lil favors for RDP 💅

🧰 utilities

• adcl — calculates ADCL for each pquery in a placefile.
• check — checks placefiles for common problems. the friend who reads your texts before you send them 🫶
• 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. just the facts, ma'am.
• islands — finds the mass islands of one or more pqueries.
• merge — merges placefiles together. friendship arc 🤝
• mft — Multi-Filter and Transform placefiles. multitasking queen.
• 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. un-deduping, because sometimes you need the twins back 🙈
• 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 — go on, she doesn't bite 💖

⭐ 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). peace and quiet era 🤫
• --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. king behavior fr fr 👑

okay that's the whole page bestie, tysm for reading, mwah 💖 — this was guppy version 1.1~alpha19, dated June 2020, from the User Commands section of the manual (that's manual page 1, iykyk). slay ✨🦋🎀